[gmx-users] Re: gmx-users Digest, Vol 11, Issue 19: problem with adding a carbonate molecule to .rtp file
balamurugan r
biobee at rediffmail.com
Tue Mar 8 08:06:53 CET 2005
(Davi
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=0ASir,=0A I thank you for the suggestion and it worked. When i use:=0A=
pdb2gmx -f 1D3K.pdb -o 1 -p top.top -n index.ndx -ignh , i get an error st=
ating =0A"Looking whether force field file ffG43a1.rtp exists=0AOpening lib=
rary file /usr/local/gromacs/share/top/ffG43a1.rtp=0AOpening library file /=
usr/local/gromacs/share/top/aminoacids.dat=0AReading 1D3K.pdb...=0ARead 'SE=
RUM TRANSFERRIN', 2695 atoms=0AOpening library file /usr/local/gromacs/shar=
e/top/xlateat.dat=0A23 out of 23 lines of xlateat.dat converted succesfully=
=0AAnalyzing pdb file=0AFatal error: Chain identifier 'A' was used in two n=
on-sequential blocks (residue 331, atom 2556)"=0A=0Aand i just tried using =
the -merge option with pdb2gmx and again it gave me an error message:=0A=0A=
"Checking for duplicate atoms....=0Adeleting duplicate atom O CYS2 329 =
ch A pdb nr 2551=0ANow there are 2555 atoms=0AWARNING: with the -remh opti=
on the generated index file (index.ndx) might be useless=0A(the index file =
is generated before hydrogens are added)N-terminus: NH3+=0AC-terminus: COO-=
=0ANo N- or C-terminus found: this chain appears to contain no protein=0AFa=
tal error: Atom -C not found in residue ASP1 while adding hydrogens"=0A I =
have checked all the .itp files and the changes i have made to .rtp file. =
Can you please help me.=0A=0AThank you once again=0A=0Abala=0A=0A =0A=0AOn=
Sun, 06 Mar 2005 gmx-users-request at gromacs.org wrote :=0A>Send gmx-users m=
ailing list submissions to=0A> gmx-users at gromacs.org=0A>=0A>To subscribe o=
r unsubscribe via the World Wide Web, visit=0A> http://www.gromacs.org/mai=
lman/listinfo/gmx-users=0A>or, via email, send a message with subject or bo=
dy 'help' to=0A> gmx-users-request at gromacs.org=0A>=0A>You can reach the pe=
rson managing the list at=0A> gmx-users-owner at gromacs.org=0A>=0A>When repl=
ying, please edit your Subject line so it is more specific=0A>than "Re: Con=
tents of gmx-users digest..."=0A>=0A>=0A>Today's Topics:=0A>=0A> 1. nonb=
onded LJ-parameters (Stephan Dammer)=0A> 2. Re: nonbonded LJ-parameters =
(David van der Spoel)=0A> 3. Re: Potentials for Ions (Marc Baaden)=0A> =
4. problem with adding a carbonate molecule to .rtp file=0A> (bala=
murugan r)=0A> 5. Re: problem with adding a carbonate molecule to .rtp f=
ile=0A> (David van der Spoel)=0A>=0A>=0A>----------------------------=
------------------------------------------=0A>=0A>Message: 1=0A>Date: Sat, =
5 Mar 2005 14:00:41 +0100 (CET)=0A> From: Stephan Dammer <S.M.Dammer at tnw.ut=
wente.nl>=0A>Subject: [gmx-users] nonbonded LJ-parameters=0A>To: gmx-users@=
gromacs.org=0A>Message-ID: <Pine.LNX.4.58.0503051345070.19894 at parmesan>=0A>=
Content-Type: TEXT/PLAIN; charset=3DUS-ASCII=0A>=0A>Hi,=0A>=0A>I have a rem=
ark/question concerning the use of nonbonded LJ-parameters in=0A>GROMACS.=
=0A>=0A>Assume you simulate a mixture of "artificial" gas and liquid atoms.=
The=0A>beginning of your topology file could look like this:=0A>=0A>;;;;;;=
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;=0A>[ defa=
ults ]=0A>; nbfunc 1:LJ comb-rule: provide LJ parameters sigma and epsilo=
n=0A>1 3=0A>=0A>[ atomtypes ]=0A>; name mass cha=
rge ptype sigma epsilon=0A>GAS 40.000 0.000 A=
0.34 1.0=0A>LIQ 20.00 0.000 A 0.=
34 3.0=0A>;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;=
;;;;;;;;;;;=0A>=0A>Due to combination rule =3D 3 the LJ-parameters are sigm=
a and epsilon, (and=0A>not C_6 and C_12). If you do not want to use the com=
bination rule 3 to=0A>determine the LJ-parameters for interactions between =
GAS and LIQ atoms,=0A>you have to provide interaction parameters yourself i=
n the=0A>"nonbonded_params" part of the topology file. As far as I understo=
od the=0A>manual, using combination rule 3 determines that these interactio=
n=0A>parameters are sigma_GAS_LIQ and epsilon_GAS_LIQ. However, it seems th=
at=0A>if you provide these LJ-parameters as sigma and epsilon (as was done =
for=0A>the GAS-GAS and LIQ-LIQ interactions) this will NOT work (at least=
=0A>according to a simple check I performed). Hence, something like=0A>=0A>=
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;=0A>[ =
nonbond_params]=0A>; i j func sigma epsilon, func=3D1=3DLJ=
=0A> GAS LIQ 1 0.34 0.01=0A>;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;=
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;=0A>=0A>will NOT lead to interaction p=
arameters sigma_GAS_LIQ=3D0.34=0A>epsilon_GAS_LIQ=3D0.01. Instead, (as far =
as I could check it) one has to=0A>provide the LJ-parameters C_6 and C_12 f=
or the GAS-LIQ interactions=0A>=0A>;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;=
;;;;;;;;;;;;;;;;;;;;;;;;;;;=0A>[ nonbond_params]=0A>; i j func =
C_6 C_12=0A> GAS LIQ 1 6.179217664e-5 9.5456827=
36e-8=0A>;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;=
;=0A>=0A>although for GAS-GAS and LIQ-LIQ interactions epsilon and sigma ar=
e used.=0A>=0A>I posted this, because I do not know if this behavior is wan=
ted (and I=0A>simply misunderstood the manual), or whether this perhaps sho=
uld be fixed.=0A>Moreover, maybe others have stepped upon the same problem.=
=0A>=0A>Best regards,=0A>Stephan=0A>=0A>ps: I use GROMACS 3.2.1=0A>--------=
------------------------------------------------------------------=0A>Steph=
an M. Dammer University of Twente=0A>e-mail: s.=
m.dammer at tnw.utwente.nl Physics of Fluids=0A>web: http://stilto=
n.tnw.utwente.nl/~dammer/ P.O. Box 217, 7500 AE Enschede=0A>telefone: [+3=
1] (53) 489 2486 The Netherlands=0A>fax: [+31] (53) 48=
9 8068 room: CT-A 124=0A>=0A>=0A>--------------------------=
----=0A>=0A>Message: 2=0A>Date: Sat, 05 Mar 2005 14:11:32 +0100=0A> From: D=
avid van der Spoel <spoel at xray.bmc.uu.se>=0A>Subject: Re: [gmx-users] nonbo=
nded LJ-parameters=0A>To: Discussion list for GROMACS users <gmx-users at grom=
acs.org>=0A>Message-ID: <1110028292.5759.41.camel at vangogh>=0A>Content-Type:=
text/plain=0A>=0A>On Sat, 2005-03-05 at 14:00 +0100, Stephan Dammer wrote:=
=0A> > Hi,=0A> >=0A>=0A> > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;=
;;;;;;;;;;;;;;;;;;;=0A> > [ nonbond_params]=0A> > ; i j func C=
_6 C_12=0A> > GAS LIQ 1 6.179217664e-5 9.5456827=
36e-8=0A> > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;=
;;;;=0A> >=0A> > although for GAS-GAS and LIQ-LIQ interactions epsilon and =
sigma are used.=0A>=0A>I think this analysis is correct, and acknowledge th=
at it may be=0A>confusing. Therefore it is important to check what you get =
after running=0A>grompp, using the gmxdump program. This applies for anythi=
ng but the=0A>standard pdb2gmx-generated topologies. So:=0A>gmxdump -s topo=
l.tpr | more=0A>and then search for "idef" which is the structure holding t=
he C6 and C12=0A>parameters.=0A>=0A>=0A> >=0A> > I posted this, because I d=
o not know if this behavior is wanted (and I=0A> > simply misunderstood the=
manual), or whether this perhaps should be fixed.=0A> > Moreover, maybe ot=
hers have stepped upon the same problem.=0A> >=0A> > Best regards,=0A> > St=
ephan=0A> >=0A> > ps: I use GROMACS 3.2.1=0A> > ---------------------------=
-----------------------------------------------=0A> > Stephan M. Dammer =
University of Twente=0A> > e-mail: s.m.dammer at tnw.=
utwente.nl Physics of Fluids=0A> > web: http://stilton.tnw.utwe=
nte.nl/~dammer/ P.O. Box 217, 7500 AE Enschede=0A> > telefone: [+31] (53)=
489 2486 The Netherlands=0A> > fax: [+31] (53) 489 80=
68 room: CT-A 124=0A> > ___________________________________=
____________=0A> > gmx-users mailing list=0A> > gmx-users at gromacs.org=0A> >=
http://www.gromacs.org/mailman/listinfo/gmx-users=0A> > Please don't post =
(un)subscribe requests to the list. Use the=0A> > www interface or send it =
to gmx-users-request at gromacs.org.=0A>--=0A>David.=0A>______________________=
__________________________________________________=0A>David van der Spoel, =
PhD, Assoc. Prof., Molecular Biophysics group,=0A>Dept. of Cell and Molecul=
ar Biology, Uppsala University.=0A>Husargatan 3, Box 596, 75124 Up=
psala, Sweden=0A>phone: 46 18 471 4205 fax: 46 18 511 755=0A>spoe=
l at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel=0A>+++=
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++=0A>=
=0A>--=0A>David.=0A>_______________________________________________________=
_________________=0A>David van der Spoel, PhD, Assoc. Prof., Molecular Biop=
hysics group,=0A>Dept. of Cell and Molecular Biology, Uppsala University.=
=0A>Husargatan 3, Box 596, 75124 Uppsala, Sweden=0A>phone: 46 18 =
471 4205 fax: 46 18 511 755=0A>spoel at xray.bmc.uu.se spoel at groma=
cs.org http://xray.bmc.uu.se/~spoel=0A>++++++++++++++++++++++++++++++++++=
++++++++++++++++++++++++++++++++++++++=0A>=0A>=0A>=0A>=0A>-----------------=
-------------=0A>=0A>Message: 3=0A>Date: Sat, 05 Mar 2005 19:44:02 +0100=0A=
> From: Marc Baaden <baaden at smplinux.de>=0A>Subject: Re: [gmx-users] Potent=
ials for Ions=0A>To: Discussion list for GROMACS users <gmx-users at gromacs.o=
rg>=0A>Message-ID: <200503051844.j25Ii2DT011770 at apex.ibpc.fr>=0A>Content-Ty=
pe: text/plain; charset=3Dus-ascii=0A>=0A>=0A>Dear Sowmianarayanan,=0A>=0A>=
I have used nitrate and perchlorate in the past (in conjunction with=0A>the=
Amber forcefield, though) and you can find the corresponding force=0A>fiel=
d parameters at several places. Either at the Amber parameter database=0A>w=
ebsite [1], in my PhD thesis (pages 18-28) [2] or in the corresponding=0A>r=
esearch articles [3].=0A>=0A>Good luck,=0A>Marc=0A>=0A>[1] http://pharmacy.=
man.ac.uk/amber/=0A>=0A>[2] http://www.baaden.ibpc.fr/pub/other/PhD_vol1.pd=
f=0A> http://www.baaden.ibpc.fr/pub/other/PhD_vol2.pdf=0A>=0A>[3] M. Ba=
aden, F. Berny, G. Wipff and C. Madic; "A molecular dynamics and=0A> qu=
antum mechanics study of M3+ lanthanide cation solvation by acetonitrile:=
=0A> the role of cation size, counterions and polarization effects=0A> =
investigated.", J. Phys. Chem. A, 104, 2000, 7659-7671.=0A>=0A> M. =
Baaden, M. Burgard, and G. Wipff; "TBP at the water - oil interface:=0A> =
the effect of TBP concentration and water acidity investigated by molecul=
ar=0A> dynamics simulations", J. Phys. Chem. B, 105, 2001, 11131-11141=
=0A>=0A>=0A> >>> Sowmianarayanan Rajamani said:=0A> >> Dear All,=0A> >>=
=0A> >> Can anyone please help me find the force fields for the following =
ions:=0A> >> 1. Thiocyanate (SCN-)=0A> >> 2. nitrate (NO3-)=0A> >> 3. ch=
lorate (ClO4-) or perchlorate=0A> >>=0A> >> Thank you,=0A> >> Sowmi=0A> =
>>=0A> >>=0A> >> Sowmianarayanan Rajamani=0A> >> Graduate Student=0A> =
>> Rensselaer Polytechnic Institute=0A> >> 110 8th Street=0A> >> Troy, NY=
-12180=0A> >> Ph: 518-276-3031=0A> >>=0A> >> ___________________________=
____________________=0A> >> gmx-users mailing list=0A> >> gmx-users at groma=
cs.org=0A> >> http://www.gromacs.org/mailman/listinfo/gmx-users=0A> >> Pl=
ease don't post (un)subscribe requests to the list. Use the=0A> >> www int=
erface or send it to gmx-users-request at gromacs.org.=0A> >>=0A>=0A>Marc Baa=
den=0A>=0A>--=0A> Dr. Marc Baaden - Institut de Biologie Physico-Chimique=
, Paris=0A> mailto:baaden at smplinux.de - http://www.marc-baaden.d=
e=0A> FAX: +33 15841 5026 - Tel: +33 15841 5176 ou +33 609 843217=0A>=
=0A>=0A>=0A>=0A>------------------------------=0A>=0A>Message: 4=0A>Date: 6=
Mar 2005 08:59:21 -0000=0A> From: "balamurugan r" <biobee at rediffmail.com>=
=0A>Subject: [gmx-users] problem with adding a carbonate molecule to .rtp=
=0A> file=0A>To: gmx-users at gromacs.org=0A>Message-ID: <20050306085921.1727=
1.qmail at webmail17.rediffmail.com>=0A>Content-Type: text/plain; charset=3D"i=
so-8859-1"=0A>=0A> Sir,=0A>I have a protein transferrinthat contains a Fe=
and a CO3 hetero molecule. I used the ffG43a1 force field. When i ran pdb2=
gmx i got an ERROR saying the CO3 residue was not found in the database. I =
tried to add the molecule to the datadase i got the itp file from PRODRG2 =
server :=0A>=0A>; Questions/comments to dava at davapc1.bioch.dundee.ac.=
uk=0A>;=0A>; When using this software in a publication, cite:=0A>; =
A. W. Schuettelkopf and D. M. F. van Aalten (2004).=0A>; PRODRG -=
a tool for high-throughput crystallography=0A>; of protein-ligand co=
mplexes.=0A>; Acta Crystallogr. D60, 1355--1363.=0A>;=0A>;=0A>=0A>[ m=
oleculetype ]=0A>; Name nrexcl=0A>CO3 3=0A>=0A>[ atoms ]=0A>; nr =
type resnr resid atom cgnr charge mass=0A> 1 OM =
1 CO3 OAA 1 -0.221 15.9994=0A> 2 C 1 CO3 =
CAC 1 0.494 12.0110=0A> 3 OM 1 CO3 OAB 1 =
-0.221 15.9994=0A> 4 OM 1 CO3 OAD 1 -0.052 15=
.9994=0A>=0A>[ bonds ]=0A>; ai aj fu c0, c1, ...=0A> 1 2 1 0=
.125 418400.0 0.125 418400.0 ; OAA CAC=0A> 2 3 1 0.12=
5 418400.0 0.125 418400.0 ; CAC OAB=0A> 2 4 1 0.125 =
418400.0 0.125 418400.0 ; CAC OAD=0A>=0A>[ pairs ]=0A>; ai aj =
fu c0, c1, ...=0A>=0A>[ angles ]=0A>; ai aj ak fu c0, c1, ...=0A> =
1 2 3 1 126.0 502.1 126.0 502.1 ; OAA CAC OA=
B=0A> 1 2 4 1 126.0 502.1 126.0 502.1 ; OAA C=
AC OAD=0A> 3 2 4 1 126.0 502.1 126.0 502.1 ; =
OAB CAC OAD=0A>=0A>[ dihedrals ]=0A>; ai aj ak al fu c0, c1, m, ..=
.=0A> 2 4 3 1 2 0.0 1673.6 0 0.0 1673.6 0 ; imp CAC =
OAD OAB OAA=0A>=0A>and then i tried to update the ff<***>.rtp file by ad=
ding the following lines to the last of the .rtp file=0A>[CO3]=0A>[atoms]=
=0A>OAA OM -0.221 0=0A>CAC C 0.494 1=0A>OAB OM -0.221 0=0A>OAD OM =
-0.052 2=0A> I obtained the details from the .itp file from PRODRG2 serv=
er=0A>but still i am not able to run pdb2gmx the error is that :=0A> "Ato=
m C in residue CO3 330 not found in rtp entry with 4 atoms while sorting at=
oms "=0A>=0A> I dont know how to proceed further.=0A>please guide me wher=
e i went wrong=0A>-------------- next part --------------=0A>An HTML attach=
ment was scrubbed...=0A>URL: http://www.gromacs.org/pipermail/gmx-users/att=
achments/20050306/f71f7708/attachment-0001.htm=0A>=0A>---------------------=
---------=0A>=0A>Message: 5=0A>Date: Sun, 06 Mar 2005 10:58:17 +0100=0A> Fr=
om: David van der Spoel <spoel at xray.bmc.uu.se>=0A>Subject: Re: [gmx-users] =
problem with adding a carbonate molecule to=0A> .rtp file=0A>To: balamurug=
an r <biobee at rediffmail.com>, Discussion list for GROMACS=0A> users <gmx-u=
sers at gromacs.org>=0A>Message-ID: <1110103097.5760.11.camel at vangogh>=0A>Cont=
ent-Type: text/plain=0A>=0A>On Sun, 2005-03-06 at 08:59 +0000, balamurugan =
r wrote:=0A> > Sir,=0A>=0A> > and then i tried to update the ff<***>.rtp =
file by adding the=0A> > following lines to the last of the .rtp file=0A> >=
[CO3]=0A> > [atoms]=0A> > OAA OM -0.221 0=0A> > CAC C 0.494 1=0A> > O=
AB OM -0.221 0=0A> > OAD OM -0.052 2=0A> > I obtained the details fro=
m the .itp file from PRODRG2 server=0A> > but still i am not able to run pd=
b2gmx the error is that :=0A> > "Atom C in residue CO3 330 not found in r=
tp entry with 4 atoms while=0A> > sorting atoms "=0A> >=0A> > I dont know=
how to proceed further.=0A> > please guide me where i went wrong=0A>You're=
almost there. The first string in the rtp entry is the atom name=0A>as it =
appears in the pdb file, the second is the atom type. You probably=0A>need =
to change the first string to match the pdb file.=0A>=0A>Besides that you n=
eed to carefully check the force field for the CO3=0A>group. I would sugges=
t you do a simulation of it in pure water as well=0A>to test whether geomet=
ry is reasonable, and e.g. hydrogen bonding=0A>distances.=0A> >=0A> >=0A> >=
=0A> >=0A> > _______________________________________________=0A> > gmx-user=
s mailing list=0A> > gmx-users at gromacs.org=0A> > http://www.gromacs.org/mai=
lman/listinfo/gmx-users=0A> > Please don't post (un)subscribe requests to t=
he list. Use the=0A> > www interface or send it to gmx-users-request at gromac=
s.org.=0A>--=0A>David.=0A>_________________________________________________=
_______________________=0A>David van der Spoel, PhD, Assoc. Prof., Molecula=
r Biophysics group,=0A>Dept. of Cell and Molecular Biology, Uppsala Univers=
ity.=0A>Husargatan 3, Box 596, 75124 Uppsala, Sweden=0A>phone: 46=
18 471 4205 fax: 46 18 511 755=0A>spoel at xray.bmc.uu.se spoel at g=
romacs.org http://xray.bmc.uu.se/~spoel=0A>++++++++++++++++++++++++++++++=
++++++++++++++++++++++++++++++++++++++++++=0A>=0A>--=0A>David.=0A>_________=
_______________________________________________________________=0A>David va=
n der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,=0A>Dept. of Cel=
l and Molecular Biology, Uppsala University.=0A>Husargatan 3, Box 596, =
75124 Uppsala, Sweden=0A>phone: 46 18 471 4205 fax: 46 18 51=
1 755=0A>spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/=
~spoel=0A>+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++=
+++++++=0A>=0A>=0A>=0A>=0A>------------------------------=0A>=0A>__________=
_____________________________________=0A>gmx-users mailing list=0A>gmx-user=
s at gromacs.org=0A>http://www.gromacs.org/mailman/listinfo/gmx-users=0A>=0A>=
=0A>End of gmx-users Digest, Vol 11, Issue 19=0A>**************************=
***************=0A
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<P>=0A <BR>=0ASir,<BR>=0A I thank you for the suggestion and it=
worked. When i use:<BR>=0A pdb2gmx -f 1D3K.pdb -o 1 -p top.top -n in=
dex.ndx -ignh , i get an error stating <BR>=0A"Looking whether force f=
ield file ffG43a1.rtp exists<BR>=0AOpening library file /usr/local/gromacs/=
share/top/ffG43a1.rtp<BR>=0AOpening library file /usr/local/gromacs/share/t=
op/aminoacids.dat<BR>=0AReading 1D3K.pdb...<BR>=0ARead 'SERUM TRANSFERRIN',=
2695 atoms<BR>=0AOpening library file /usr/local/gromacs/share/top/xlateat=
.dat<BR>=0A23 out of 23 lines of xlateat.dat converted succesfully<BR>=0AAn=
alyzing pdb file<BR>=0AFatal error: Chain identifier 'A' was used in two no=
n-sequential blocks (residue 331, atom 2556)"<BR>=0A<BR>=0Aand i just =
tried using the -merge option with pdb2gmx and again it gave me an error me=
ssage:<BR>=0A<BR>=0A"Checking for duplicate atoms....<BR>=0Adeleting d=
uplicate atom O CYS2 329 ch A pdb nr 2551<BR>=0ANo=
w there are 2555 atoms<BR>=0AWARNING: with the -remh option the generated i=
ndex file (index.ndx) might be useless<BR>=0A(the index file is generated b=
efore hydrogens are added)N-terminus: NH3+<BR>=0AC-terminus: COO-<BR>=0ANo =
N- or C-terminus found: this chain appears to contain no protein<BR>=0AFata=
l error: Atom -C not found in residue ASP1 while adding hydrogens"<BR>=
=0A I have checked all the .itp files and the changes i have made to =
.rtp file. Can you please help me.<BR>=0A<BR>=0AThank you once =
again<BR>=0A<BR>=0Abala<BR>=0A<BR>=0A <BR>=0A<BR>=0AOn Sun, 06 Mar 2005 gmx=
-users-request at gromacs.org wrote :<BR>=0A>Send gmx-users mailing list su=
bmissions to<BR>=0A> gmx-users at gromacs.org<BR>=0A>=
;<BR>=0A>To subscribe or unsubscribe via the World Wide Web, visit<BR>=
=0A> http://www.gromacs.org/mailman/listinfo/gmx-use=
rs<BR>=0A>or, via email, send a message with subject or body 'help' to<B=
R>=0A> gmx-users-request at gromacs.org<BR>=0A><BR>=
=0A>You can reach the person managing the list at<BR>=0A> &nbs=
p; gmx-users-owner at gromacs.org<BR>=0A><BR>=0A>When replying, pl=
ease edit your Subject line so it is more specific<BR>=0A>than "Re:=
Contents of gmx-users digest..."<BR>=0A><BR>=0A><BR>=0A>Toda=
y's Topics:<BR>=0A><BR>=0A> 1. nonbonded LJ-parameters (=
Stephan Dammer)<BR>=0A> 2. Re: nonbonded LJ-parameters (Dav=
id van der Spoel)<BR>=0A> 3. Re: Potentials for Ions =
(Marc Baaden)<BR>=0A> 4. problem with adding a carbonate mo=
lecule to .rtp file<BR>=0A> (balamurugan r)<BR>=0A&=
gt; 5. Re: problem with adding a carbonate molecule to .rtp fi=
le<BR>=0A> (David van der Spoel)<BR>=0A><BR>=0A&=
gt;<BR>=0A>-------------------------------------------------------------=
---------<BR>=0A><BR>=0A>Message: 1<BR>=0A>Date: Sat, 5 Mar 2005 1=
4:00:41 +0100 (CET)<BR>=0A> From: Stephan Dammer <S.M.Dammer at tnw.utwe=
nte.nl><BR>=0A>Subject: [gmx-users] nonbonded LJ-parameters<BR>=0A>=
;To: gmx-users at gromacs.org<BR>=0A>Message-ID: <Pine.LNX.4.58.05030513=
45070.19894 at parmesan><BR>=0A>Content-Type: TEXT/PLAIN; charset=3DUS-A=
SCII<BR>=0A><BR>=0A>Hi,<BR>=0A><BR>=0A>I have a remark/question=
concerning the use of nonbonded LJ-parameters in<BR>=0A>GROMACS.<BR>=0A=
><BR>=0A>Assume you simulate a mixture of "artificial" gas =
and liquid atoms. The<BR>=0A>beginning of your topology file could look =
like this:<BR>=0A><BR>=0A>;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;=
;;;;;;;;;;;;;;;;;;;;;;;;;;;;<BR>=0A>[ defaults ]<BR>=0A>; nbfunc 1:LJ=
comb-rule: provide LJ parameters sigma and epsilon<BR>=0A>1 =
; 3<BR>=0A><BR>=0A>[ atomt=
ypes ]<BR>=0A>; name mass =
charge ptype sigma epsilon=
<BR>=0A>GAS 40.000 0.00=
0 A 0.34  =
; 1.0<BR>=0A>LIQ 20.00 &=
nbsp; 0.000 A 0.34 &n=
bsp; 3.0<BR>=0A>;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;=
;;;;;;;;;;;;;;;;;;;;;;<BR>=0A><BR>=0A>Due to combination rule =3D 3 t=
he LJ-parameters are sigma and epsilon, (and<BR>=0A>not C_6 and C_12). I=
f you do not want to use the combination rule 3 to<BR>=0A>determine the =
LJ-parameters for interactions between GAS and LIQ atoms,<BR>=0A>you hav=
e to provide interaction parameters yourself in the<BR>=0A>"nonbond=
ed_params" part of the topology file. As far as I understood the<BR>=
=0A>manual, using combination rule 3 determines that these interaction<B=
R>=0A>parameters are sigma_GAS_LIQ and epsilon_GAS_LIQ. However, it seem=
s that<BR>=0A>if you provide these LJ-parameters as sigma and epsilon (a=
s was done for<BR>=0A>the GAS-GAS and LIQ-LIQ interactions) this will NO=
T work (at least<BR>=0A>according to a simple check I performed). Hence,=
something like<BR>=0A><BR>=0A>;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;=
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<BR>=0A>[ nonbond_params]<BR>=0A>; i&n=
bsp; j func sigma epsilon,=
func=3D1=3DLJ<BR>=0A> GAS LIQ 1  =
; 0.34 0.01<BR>=0A>;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;=
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<BR>=0A><BR>=0A>will NOT lead to intera=
ction parameters sigma_GAS_LIQ=3D0.34<BR>=0A>epsilon_GAS_LIQ=3D0.01. Ins=
tead, (as far as I could check it) one has to<BR>=0A>provide the LJ-para=
meters C_6 and C_12 for the GAS-LIQ interactions<BR>=0A><BR>=0A>;;;;;=
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<BR>=0A>[ =
nonbond_params]<BR>=0A>; i j func&nbs=
p; C_6 C_12<BR>=0A>&nbs=
p; GAS LIQ 1 6.179217664e-5 =
; 9.545682736e-8<BR>=0A>;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;=
;;;;;;;;;;;;;;;;;;;<BR>=0A><BR>=0A>although for GAS-GAS and LIQ-LIQ i=
nteractions epsilon and sigma are used.<BR>=0A><BR>=0A>I posted this,=
because I do not know if this behavior is wanted (and I<BR>=0A>simply m=
isunderstood the manual), or whether this perhaps should be fixed.<BR>=0A&g=
t;Moreover, maybe others have stepped upon the same problem.<BR>=0A><BR>=
=0A>Best regards,<BR>=0A>Stephan<BR>=0A><BR>=0A>ps: I use GROMA=
CS 3.2.1<BR>=0A>--------------------------------------------------------=
------------------<BR>=0A>Stephan M. Dammer &=
nbsp; Unive=
rsity of Twente<BR>=0A>e-mail: s.m.dammer at tnw.utwente.nl &n=
bsp; Physics of Fluids<BR>=0A>web: http://stilton.=
tnw.utwente.nl/~dammer/ P.O. Box 217, 7500 AE Enschede<BR>=0A>tel=
efone: [+31] (53) 489 2486 =
The Netherlands<BR>=0A>fax: [+31] (53) 489 8=
068 room: CT-A 124<=
BR>=0A><BR>=0A><BR>=0A>------------------------------<BR>=0A><B=
R>=0A>Message: 2<BR>=0A>Date: Sat, 05 Mar 2005 14:11:32 +0100<BR>=0A&=
gt; From: David van der Spoel <spoel at xray.bmc.uu.se><BR>=0A>Subjec=
t: Re: [gmx-users] nonbonded LJ-parameters<BR>=0A>To: Discussion list fo=
r GROMACS users <gmx-users at gromacs.org><BR>=0A>Message-ID: <111=
0028292.5759.41.camel at vangogh><BR>=0A>Content-Type: text/plain<BR>=0A=
><BR>=0A>On Sat, 2005-03-05 at 14:00 +0100, Stephan Dammer wrote:<BR>=
=0A> > Hi,<BR>=0A> ><BR>=0A><BR>=0A> > ;;;;;;;;;;;;;;;=
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<BR>=0A> > [ nonb=
ond_params]<BR>=0A> > ; i j func&n=
bsp; C_6 C_12<BR>=0A> &=
gt; GAS LIQ 1 6.179217664e=
-5 9.545682736e-8<BR>=0A> > ;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;=
;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;<BR>=0A> ><BR>=0A> > although f=
or GAS-GAS and LIQ-LIQ interactions epsilon and sigma are used.<BR>=0A><=
BR>=0A>I think this analysis is correct, and acknowledge that it may be<=
BR>=0A>confusing. Therefore it is important to check what you get after =
running<BR>=0A>grompp, using the gmxdump program. This applies for anyth=
ing but the<BR>=0A>standard pdb2gmx-generated topologies. So:<BR>=0A>=
gmxdump -s topol.tpr | more<BR>=0A>and then search for "idef" =
which is the structure holding the C6 and C12<BR>=0A>parameters.<BR>=0A&=
gt;<BR>=0A><BR>=0A> ><BR>=0A> > I posted this, because I do =
not know if this behavior is wanted (and I<BR>=0A> > simply misunders=
tood the manual), or whether this perhaps should be fixed.<BR>=0A> > =
Moreover, maybe others have stepped upon the same problem.<BR>=0A> ><=
BR>=0A> > Best regards,<BR>=0A> > Stephan<BR>=0A> ><BR>=
=0A> > ps: I use GROMACS 3.2.1<BR>=0A> > ----------------------=
----------------------------------------------------<BR>=0A> > Stepha=
n M. Dammer &=
nbsp; University of Twente<BR>=0A> > e-m=
ail: s.m.dammer at tnw.utwente.nl Ph=
ysics of Fluids<BR>=0A> > web: http://stilton.tnw.utwente.nl/~dammer/=
P.O. Box 217, 7500 AE Enschede<BR>=0A> > telefone: [+31] (53)=
489 2486 The Nethe=
rlands<BR>=0A> > fax: [+31] (53) 489 8068 &=
nbsp; room: CT-A 124<BR>=0A> =
> _______________________________________________<BR>=0A> > gmx-us=
ers mailing list<BR>=0A> > gmx-users at gromacs.org<BR>=0A> > http=
://www.gromacs.org/mailman/listinfo/gmx-users<BR>=0A> > Please don't =
post (un)subscribe requests to the list. Use the<BR>=0A> > www interf=
ace or send it to gmx-users-request at gromacs.org.<BR>=0A>--<BR>=0A>Dav=
id.<BR>=0A>_____________________________________________________________=
___________<BR>=0A>David van der Spoel, PhD, Assoc. Prof., Molecular Bio=
physics group,<BR>=0A>Dept. of Cell and Molecular Biology, Uppsala Unive=
rsity.<BR>=0A>Husargatan 3, Box 596, 7=
5124 Uppsala, Sweden<BR>=0A>phone: 46 18 471 4205 &nb=
sp; fax: 46 18 511 755<BR>=0A>spoel at xray.bmc.uu.se &=
nbsp; spoel at gromacs.org http://xray.bmc.uu.se/~spoel<BR>=0A>+++++=
+++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<BR>=0A&=
gt;<BR>=0A>--<BR>=0A>David.<BR>=0A>_______________________________=
_________________________________________<BR>=0A>David van der Spoel, Ph=
D, Assoc. Prof., Molecular Biophysics group,<BR>=0A>Dept. of Cell and Mo=
lecular Biology, Uppsala University.<BR>=0A>Husargatan 3, Box 596, =
75124 Uppsala, Sweden<BR>=0A>phone: 4=
6 18 471 4205 fax: 46 18 511 755<BR>=0A&g=
t;spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bm=
c.uu.se/~spoel<BR>=0A>++++++++++++++++++++++++++++++++++++++++++++++++++=
++++++++++++++++++++++<BR>=0A><BR>=0A><BR>=0A><BR>=0A><BR>=0A&g=
t;------------------------------<BR>=0A><BR>=0A>Message: 3<BR>=0A>=
Date: Sat, 05 Mar 2005 19:44:02 +0100<BR>=0A> From: Marc Baaden <baad=
en at smplinux.de><BR>=0A>Subject: Re: [gmx-users] Potentials for Ions<B=
R>=0A>To: Discussion list for GROMACS users <gmx-users at gromacs.org>=
;<BR>=0A>Message-ID: <200503051844.j25Ii2DT011770 at apex.ibpc.fr><BR=
>=0A>Content-Type: text/plain; charset=3Dus-ascii<BR>=0A><BR>=0A><=
BR>=0A>Dear Sowmianarayanan,<BR>=0A><BR>=0A>I have used nitrate an=
d perchlorate in the past (in conjunction with<BR>=0A>the Amber forcefie=
ld, though) and you can find the corresponding force<BR>=0A>field parame=
ters at several places. Either at the Amber parameter database<BR>=0A>we=
bsite [1], in my PhD thesis (pages 18-28) [2] or in the corresponding<BR>=
=0A>research articles [3].<BR>=0A><BR>=0A>Good luck,<BR>=0A>Mar=
c<BR>=0A><BR>=0A>[1] http://pharmacy.man.ac.uk/amber/<BR>=0A><BR>=
=0A>[2] http://www.baaden.ibpc.fr/pub/other/PhD_vol1.pdf<BR>=0A> =
; http://www.baaden.ibpc.fr/pub/other/PhD_vol2.pdf<BR>=0A><BR>=
=0A>[3] M. Baaden, F. Berny, G. Wipff and C. Madic; "A molecular dy=
namics and<BR>=0A> quantum mechanics study of M3+ lanthani=
de cation solvation by acetonitrile:<BR>=0A> the role of c=
ation size, counterions and polarization effects<BR>=0A> i=
nvestigated.", J. Phys. Chem. A, 104, 2000, 7659-7671.<BR>=0A><BR>=
=0A> M. Baaden, M. Burgard, and G. Wipff; "TBP at the=
water - oil interface:<BR>=0A> the effect of TBP concentr=
ation and water acidity investigated by molecular<BR>=0A> =
dynamics simulations", J. Phys. Chem. B, 105, 2001, 11131-11141<BR>=0A=
><BR>=0A><BR>=0A> >>> Sowmianarayanan Rajamani said:<BR>=
=0A> >> Dear All,<BR>=0A> >><BR>=0A> =
>> Can anyone please help me find the force fields for the following=
ions:<BR>=0A> >> 1. Thiocyanate (SCN-)<BR>=0A> >=
;> 2. nitrate (NO3-)<BR>=0A> >> 3. chlorate (ClO4-) or pe=
rchlorate<BR>=0A> >><BR>=0A> >> Thank you,<BR=
>=0A> >> Sowmi<BR>=0A> >><BR>=0A> &g=
t;><BR>=0A> >> Sowmianarayanan Rajamani<BR>=0A> =
>> Graduate Student<BR>=0A> >> Rensselaer Polytechnic =
Institute<BR>=0A> >> 110 8th Street<BR>=0A> >>=
; Troy, NY-12180<BR>=0A> >> Ph: 518-276-3031<BR>=0A> =
; >><BR>=0A> >> ______________________________________=
_________<BR>=0A> >> gmx-users mailing list<BR>=0A> =
>> gmx-users at gromacs.org<BR>=0A> >> http://www.gromac=
s.org/mailman/listinfo/gmx-users<BR>=0A> >> Please don't pos=
t (un)subscribe requests to the list. Use the<BR>=0A> >> www=
interface or send it to gmx-users-request at gromacs.org.<BR>=0A> &g=
t;><BR>=0A><BR>=0A>Marc Baaden<BR>=0A><BR>=0A>--<BR>=0A>&=
nbsp; Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris<=
BR>=0A> mailto:baaden at smplinux.de - &nbs=
p; http://www.marc-baaden.de<BR>=0A> FAX: +33 15841 5026&nb=
sp; - Tel: +33 15841 5176 ou +33 609 843217<BR>=0A><BR=
>=0A><BR>=0A><BR>=0A><BR>=0A>------------------------------<BR>=
=0A><BR>=0A>Message: 4<BR>=0A>Date: 6 Mar 2005 08:59:21 -0000<BR>=
=0A> From: "balamurugan r" <biobee at rediffmail.com><BR>=
=0A>Subject: [gmx-users] problem with adding a carbonate molecule to .rt=
p<BR>=0A> file<BR>=0A>To: gmx-users at gromacs.org<B=
R>=0A>Message-ID: <20050306085921.17271.qmail at webmail17.rediffmail.co=
m><BR>=0A>Content-Type: text/plain; charset=3D"iso-8859-1"<=
BR>=0A><BR>=0A> Sir,<BR>=0A>I have a protein transferrintha=
t contains a Fe and a CO3 hetero molecule. I used the ffG43a1 force field. =
When i ran pdb2gmx i got an ERROR saying the CO3 residue was not found in t=
he database. I tried to add the molecule to the datadase i got the itp file=
from PRODRG2 server :<BR>=0A><BR>=0A>; Qu=
estions/comments to dava at davapc1.bioch.dundee.ac.uk<BR>=0A>;<BR>=0A>;=
When using this software in a publication, cite:<BR>=
=0A>; A. W. Schuettelkopf and D. M. F. van Aalten (=
2004).<BR>=0A>; PRODRG - a tool for high-throughput=
crystallography<BR>=0A>; of protein-ligand complex=
es.<BR>=0A>; Acta Crystallogr. D60, 1355--1363.<BR>=
=0A>;<BR>=0A>;<BR>=0A><BR>=0A>[ moleculetype ]<BR>=0A>; Name=
nrexcl<BR>=0A>CO3 3<BR>=0A><BR>=0A>[ atoms ]<=
BR>=0A>; nr type resnr resid atom=
cgnr charge mass<BR>=0A> =
1 OM 1 CO3 OA=
A 1 -0.221 15.9994<BR>=0A>  =
; 2 C 1 CO3 C=
AC 1 0.494 12.0110<BR>=0A> =
3 OM 1 CO3 &nb=
sp; OAB 1 -0.221 15.9994<BR>=0A>  =
; 4 OM 1 CO3 &n=
bsp; OAD 1 -0.052 15.9994<BR>=0A><BR>=0A>=
[ bonds ]<BR>=0A>; ai aj fu c0, c1, ...<BR>=0A&=
gt; 1 2 1 0.125 418400=
.0 0.125 418400.0 ; OAA CAC<BR>=0A&g=
t; 2 3 1 0.125 418400.=
0 0.125 418400.0 ; CAC OAB<BR>=0A>=
; 2 4 1 0.125 418400.0=
0.125 418400.0 ; CAC OAD<BR>=0A>=
<BR>=0A>[ pairs ]<BR>=0A>; ai aj fu c0, c1, =
...<BR>=0A><BR>=0A>[ angles ]<BR>=0A>; ai aj ak =
fu c0, c1, ...<BR>=0A> 1 2 3&nbs=
p; 1 126.0 502.1 126.0 =
; 502.1 ; OAA CAC OAB<BR>=0A> &n=
bsp; 1 2 4 1 126.0 5=
02.1 126.0 502.1 ; OAA CAC&n=
bsp; OAD<BR>=0A> 3 2 4 1 =
126.0 502.1 126.0 50=
2.1 ; OAB CAC OAD<BR>=0A><BR>=0A>[ dihedrals ]<BR>=
=0A>; ai aj ak al fu c0, c1, m, ...=
<BR>=0A> 2 4 3 1 2 =
0.0 1673.6 0 0.0 1673.6 0 ; imp CAC =
; OAD OAB OAA<BR>=0A><BR>=0A>and then i tried to update t=
he ff<***>.rtp file by adding the following lines to the last of the =
.rtp file<BR>=0A>[CO3]<BR>=0A>[atoms]<BR>=0A>OAA OM -0.221&n=
bsp; 0<BR>=0A>CAC C 0.494 1<BR>=0A>OAB OM&nb=
sp; -0.221 0<BR>=0A>OAD OM -0.052 2<BR>=0A> I obta=
ined the details from the .itp file from PRODRG2 server<BR>=0A>but still=
i am not able to run pdb2gmx the error is that :<BR>=0A> "A=
tom C in residue CO3 330 not found in rtp entry with 4 atoms while sorting =
atoms "<BR>=0A><BR>=0A> I dont know how to proceed furthe=
r.<BR>=0A>please guide me where i went wrong<BR>=0A>-------------- ne=
xt part --------------<BR>=0A>An HTML attachment was scrubbed...<BR>=0A&=
gt;URL: http://www.gromacs.org/pipermail/gmx-users/attachments/20050306/f71=
f7708/attachment-0001.htm<BR>=0A><BR>=0A>----------------------------=
--<BR>=0A><BR>=0A>Message: 5<BR>=0A>Date: Sun, 06 Mar 2005 10:58:1=
7 +0100<BR>=0A> From: David van der Spoel <spoel at xray.bmc.uu.se><B=
R>=0A>Subject: Re: [gmx-users] problem with adding a carbonate molecule =
to<BR>=0A> .rtp file<BR>=0A>To: balamurugan r <=
;biobee at rediffmail.com>, Discussion list for GROMACS<=
BR>=0A> users <gmx-users at gromacs.org><BR>=0A&g=
t;Message-ID: <1110103097.5760.11.camel at vangogh><BR>=0A>Content-Ty=
pe: text/plain<BR>=0A><BR>=0A>On Sun, 2005-03-06 at 08:59 +0000, bala=
murugan r wrote:<BR>=0A> > Sir,<BR>=0A><BR>=0A> > and=
then i tried to update the ff<***>.rtp file by adding the<BR>=0A>=
> following lines to the last of the .rtp file<BR>=0A> > [CO3]<BR=
>=0A> > [atoms]<BR>=0A> > OAA OM -0.221 0<BR>=0A>=
; > CAC C 0.494 1<BR>=0A> > OAB OM -=
0.221 0<BR>=0A> > OAD OM -0.052 2<BR>=0A> > =
I obtained the details from the .itp file from PRODRG2 server<BR>=0A> &g=
t; but still i am not able to run pdb2gmx the error is that :<BR>=0A> &g=
t; "Atom C in residue CO3 330 not found in rtp entry with 4 ato=
ms while<BR>=0A> > sorting atoms "<BR>=0A> ><BR>=0A> &g=
t; I dont know how to proceed further.<BR>=0A> > please guide =
me where i went wrong<BR>=0A>You're almost there. The first string in th=
e rtp entry is the atom name<BR>=0A>as it appears in the pdb file, the s=
econd is the atom type. You probably<BR>=0A>need to change the first str=
ing to match the pdb file.<BR>=0A><BR>=0A>Besides that you need to ca=
refully check the force field for the CO3<BR>=0A>group. I would suggest =
you do a simulation of it in pure water as well<BR>=0A>to test whether g=
eometry is reasonable, and e.g. hydrogen bonding<BR>=0A>distances.<BR>=
=0A> ><BR>=0A> ><BR>=0A> ><BR>=0A> ><BR>=0A> >=
; _______________________________________________<BR>=0A> > gmx-users=
mailing list<BR>=0A> > gmx-users at gromacs.org<BR>=0A> > http://=
www.gromacs.org/mailman/listinfo/gmx-users<BR>=0A> > Please don't pos=
t (un)subscribe requests to the list. Use the<BR>=0A> > www interface=
or send it to gmx-users-request at gromacs.org.<BR>=0A>--<BR>=0A>David.=
<BR>=0A>________________________________________________________________=
________<BR>=0A>David van der Spoel, PhD, Assoc. Prof., Molecular Biophy=
sics group,<BR>=0A>Dept. of Cell and Molecular Biology, Uppsala Universi=
ty.<BR>=0A>Husargatan 3, Box 596, 7512=
4 Uppsala, Sweden<BR>=0A>phone: 46 18 471 4205 =
fax: 46 18 511 755<BR>=0A>spoel at xray.bmc.uu.se &nbs=
p; spoel at gromacs.org http://xray.bmc.uu.se/~spoel<BR>=0A>++++++++=
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++<BR>=0A>=
<BR>=0A>--<BR>=0A>David.<BR>=0A>__________________________________=
______________________________________<BR>=0A>David van der Spoel, PhD, =
Assoc. Prof., Molecular Biophysics group,<BR>=0A>Dept. of Cell and Molec=
ular Biology, Uppsala University.<BR>=0A>Husargatan 3, Box 596, &n=
bsp; 75124 Uppsala, Sweden<BR>=0A>phone: 46 1=
8 471 4205 fax: 46 18 511 755<BR>=0A>s=
poel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.u=
u.se/~spoel<BR>=0A>+++++++++++++++++++++++++++++++++++++++++++++++++++++=
+++++++++++++++++++<BR>=0A><BR>=0A><BR>=0A><BR>=0A><BR>=0A>-=
-----------------------------<BR>=0A><BR>=0A>________________________=
_______________________<BR>=0A>gmx-users mailing list<BR>=0A>gmx-user=
s at gromacs.org<BR>=0A>http://www.gromacs.org/mailman/listinfo/gmx-users<B=
R>=0A><BR>=0A><BR>=0A>End of gmx-users Digest, Vol 11, Issue 19<BR=
>=0A>*****************************************<BR>=0A=0A</P>=0A<br><br>=
=0A<A target=3D"_blank" HREF=3D"http://clients.rediff.com/signature/track_s=
ig.asp"><IMG SRC=3D"http://ads.rediff.com/RealMedia/ads/adstream_nx.cgi/www=
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