[gmx-users] Error while doing EM in DMSO.
Anil Kumar
anil at chem.iitb.ac.in
Wed May 16 18:47:13 CEST 2007
Dear Users,
First of all thank you Mark, yes you are right. it was problem of force
field and topoloy file mismatch.
I have made changes in the ffG43a1 residue toplogy file for DMSO., but
still getting the same error. Please let me know if i am doing some
mistake.
*******************changes made***********************
[ DMSO ]
[ atoms ]
SD SD 0.13900 0
OD OD -0.45900 0
CD1 CD 0.16000 0
CD2 CD 0.16000 0
[ bonds ]
SD OD gb_38
SD CD1 gb_39
SD CD2 gb_39
OD CD1 gb_44
OD CD2 gb_44
CD1 CD2 gb_45
[ angles ]
; ai aj ak gromos type
[ impropers ]
; ai aj ak al gromos type
[ dihedrals ]
; ai aj ak al gromos type
*********************DMSO before changes**********************
[ DMSO ]
[ atoms ]
SDmso SDMSO 0.13900 0
ODmso ODMSO -0.45900 0
CDms1 CDMSO 0.16000 0
CDms2 CDMSO 0.16000 0
[ bonds ]
SDmso ODmso gb_38
SDmso CDms1 gb_39
SDmso CDms2 gb_39
ODmso CDms1 gb_44
ODmso CDms2 gb_44
CDms1 CDms2 gb_45
[ angles ]
; ai aj ak gromos type
[ impropers ]
; ai aj ak al gromos type
[ dihedrals ]
; ai aj ak al gromos type
***********************************************************
dmso.itp file which i am using for dmso is following.
********************************************************
[ moleculetype ]
; name nrexcl
DMSO 2
[ atoms ]
; nr type resnr residu atom cgnr charge
1 SD 1 DMSO SD 1 0.139
2 CD 1 DMSO CD1 1 0.16
3 OD 1 DMSO OD 1 -0.459
4 CD 1 DMSO CD2 1 0.16
[ bonds ]
; ai aj funct b0 kb
1 2 1 0.195 376560 ; kb from Methionine
1 3 1 0.153 502080 ; kb from C=O bond
1 4 1 0.195 376560
[ angles ]
; ai aj ak funct theta kt
3 1 2 1 106.75 460.240
3 1 4 1 106.75 460.240
2 1 4 1 97.40 460.240 ; kt from Methionine
[ dihedrals ]
; ai aj ak al funct xi kxi
1 2 4 3 2 35.264 334.720 ; default params
Any suggestions, hints or helps are most appreciated.
Thanks in advance,
With Regards
anil
>
> Message: 1
> Date: Sat, 12 May 2007 16:59:40 +0530 (IST)
> From: "Anil Kumar" <anil at chem.iitb.ac.in>
> Subject: [gmx-users] Error while running grompp for em (MD) in Urea To:
gmx-users at gromacs.org
> Message-ID: <34043.10.103.7.2.1178969380.squirrel at www.chem.iitb.ac.in>
Content-Type: text/plain;charset=iso-8859-1
>
> Dear All,
>
> Can anyone help me in running simulation in explicit urea.
> When i was using urea+h2o.gro and urea.itp and tried to do simulation in
explicit urea.
> After doing genbox, i am not able to do the grompp for energy
minimization
> and getting the error which is given below.
>
> I have added masses of all the atoms of urea in atommass.dat file, but
still getting the same error.
> Please help me, where does am i making the mistakes.
>
> processing coordinates...
> Warning: atom names in base.top and after_sol.gro don't match (OW - OW1)
Warning: atom names in base.top and after_sol.gro don't match (HW1 -
HW2)
> Warning: atom names in base.top and after_sol.gro don't match (HW2 -
HW3)
> Warning: atom names in base.top and after_sol.gro don't match (OW - OW1)
Warning: atom names in base.top and after_sol.gro don't match (HW1 -
HW2)
> Warning: atom names in base.top and after_sol.gro don't match (HW2 -
HW3)
> Warning: atom names in base.top and after_sol.gro don't match (OW - OW1)
Warning: atom names in base.top and after_sol.gro don't match (HW1 -
HW2)
> Warning: atom names in base.top and after_sol.gro don't match (HW2 -
HW3)
> Warning: atom names in base.top and after_sol.gro don't match (OW - OW1)
Warning: atom names in base.top and after_sol.gro don't match (HW1 -
HW2)
> Warning: atom names in base.top and after_sol.gro don't match (HW2 -
HW3)
> Warning: atom names in base.top and after_sol.gro don't match (OW - OW1)
Warning: atom names in base.top and after_sol.gro don't match (HW1 -
HW2)
> Warning: atom names in base.top and after_sol.gro don't match (HW2 -
HW3)
> Warning: atom names in base.top and after_sol.gro don't match (OW - OW1)
Warning: atom names in base.top and after_sol.gro don't match (HW1 -
HW2)
> Warning: atom names in base.top and after_sol.gro don't match (HW2 -
HW3)
> Warning: atom names in base.top and after_sol.gro don't match (OW - OW1)
Warning: atom names in base.top and after_sol.gro don't match (HW1 -
HW2)
> (more than 20 non-matching atom names)
> WARNING 3 [file "base.top", line 808]:
> 6150 non-matching atom names
> atom names from base.top will be used
> atom names from after_sol.gro will be ignored
>
> double-checking input for internal consistency...
> renumbering atomtypes...
> converting bonded parameters...
> # BONDS: 945
> # G96BONDS: 128
> # ANGLES: 1215
> # G96ANGLES: 190
> # PDIHS: 1134
> # IDIHS: 485
> # LJ14: 1242
> # SETTLE: 2050
> ERROR 4 [file "base.top", line 808]:
> atom C1 (Res UREA-11) has mass 0
>
> ERROR 5 [file "base.top", line 808]:
> atom O2 (Res UREA-11) has mass 0
>
> ERROR 6 [file "base.top", line 808]:
> atom N3 (Res UREA-11) has mass 0
>
> ERROR 7 [file "base.top", line 808]:
> atom H4 (Res UREA-11) has mass 0
>
> ERROR 8 [file "base.top", line 808]:
> atom H5 (Res UREA-11) has mass 0
>
> ERROR 9 [file "base.top", line 808]:
> atom N6 (Res UREA-11) has mass 0
>
> ERROR 10 [file "base.top", line 808]:
> atom H7 (Res UREA-11) has mass 0
>
> -------------------------------------------------------
> Program grompp, VERSION 3.3.1
> Source code file: fatal.c, line: 416
>
> Fatal error:
> Too many warnings, grompp terminated
> -------------------------------------------------------
>
> "I'm An Oakman" (Pulp Fiction)
>
> Thanks in advance.
>
> With Warm Regards
> anil
> --
> (¨`•.•´¨) Always
> `•.¸(¨`•.•´¨) Keep
> (¨`•.•´¨)¸.•´ Smiling!
> `•.¸.•´
> «•´`•.(*•.¸(`•.¸ ¸.•´)¸.•*).•´`•»
> «•´¨*•.¸¸. * ANIL *.¸¸.•*¨`•»
> «•´`•.(¸.•´(¸.•* *•.¸)`•.¸).•´`•»
>
> ANIL KUMAR(Research Scholar),
> Bio-Organic Lab No-336(2nd Floor),
> Dept. of Chemistry,I.I.T.Bombay,Powai,
> Mumbai-400076,
> Ph. No.-022-25764780(Lab)
> -----------------------------------------
> Residence:-
> Hostel#1,Room#297,IIT Bombay,Powai,
> Mumbai-400076,Ph.No.:-022-25721017(Hostel)
> -------------------------------------------------
> Web:http://chemanil.googlepages.com/
> --------------------------
> "Education is a progressive discovery of our ignorance"
>
> - Will Durant
> ----------------------------
>
>> Send gmx-users mailing list submissions to
>> gmx-users at gromacs.org
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>> Today's Topics:
>> 1. Re: CNT Potassium doping with GROMACS (George Abadir)
>> 2. Re: Cannot find fftw3f (Mark Abraham)
>> 3. Re: suggest small revision to genbox (bharat v. adkar)
>> 4. Re: suggest small revision to genbox (David van der Spoel) 5.
Error while running MD in DMSO! (Anil Kumar)
>> ----------------------------------------------------------------------
Message: 1
>> Date: Fri, 11 May 2007 18:52:43 -0700
>> From: George Abadir <georgea at ece.ubc.ca>
>> Subject: Re: [gmx-users] CNT Potassium doping with GROMACS
>> To: georgea at ece.ubc.ca, Discussion list for GROMACS users
>> <gmx-users at gromacs.org>
>> Message-ID: <46451DEB.3090800 at ece.ubc.ca>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>> Another point: is it possible to use pdb2gmx to do the job instead of
x2top? I tried and used the GROMOS96 43b1 vacuum force field (since the
doping by potassium is in vacuum), but i got the error"Residue 'CNT'
not
>> found in residue topolgy database'. I went to the 'ffg43b1.rtp' file in
the /share/top folder and defined it as '[CNT]
>> [atoms]
>> C C 0 0'
>> but still get the same error.
>> Your help is much appreciated,
>> Thank you in advance,
>> George
>> George Abadir wrote:
>>> Hi,
>>> I want to make a simulation of CNT in an environment of potassium
>>> atoms to see how they will be adsorbed on the CNT surface (this is a
way of doping carbon nanotubes). I built a .pdb file with a CNT and
some potassium atoms with random coordinates around the nanotube. When
I run x2top to have my topology file, I get the error:"No forcefield
type for atom K with 0 bond". The problem is that the atoms of
potassium should indeed be not bonded to anything at the beginning of
the simulation. Does anybody have a way to describe such a system and
avoid this error?
>>> Thank you very much in advance,
>>> Regards,
>>> George
>>> _______________________________________________
>>> gmx-users mailing list gmx-users at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
posting!
>>> Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-request at gromacs.org.
>>> Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>> ------------------------------
>> Message: 2
>> Date: Sat, 12 May 2007 12:22:41 +1000
>> From: Mark Abraham <Mark.Abraham at anu.edu.au>
>> Subject: Re: [gmx-users] Cannot find fftw3f
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <464524F1.8000503 at anu.edu.au>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>> Omovie, Sheyore John wrote:
>>> Hi,
>>> Even after following the instructions in the HowTo Cygwin and gromacs, I
>>> still come up
>>> with the configure error:Cannot find fftw3f.
>> The most likely thing is that you haven't actually followed the
instructions precisely...
>> http://www.gromacs.org/pipermail/gmx-users/2006-April/021147.html In
particular you need "--enable-float" with configure for fftw.
>>> I ahve also tried specifying the header file directory, it still doesn't
>>> work.
>> No, that wouldn't help.
>>> I would appreciate any advice on overcoming this problem.
>> In the absence of more information from you, all I can suggest is
trying
>> again :-) In extremis, re-installing cygwin has helped another user. Mark
>> ------------------------------
>> Message: 3
>> Date: Sat, 12 May 2007 12:05:44 +0530 (IST)
>> From: "bharat v. adkar" <bharat at sscu.iisc.ernet.in>
>> Subject: Re: [gmx-users] suggest small revision to genbox
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <Pine.LNX.4.64.0705121155010.19935 at sscu.iisc.ernet.in>
Content-Type: TEXT/PLAIN; charset=US-ASCII; format=flowed
>> genbox works fine for me. i use 3.3.1 version. it works fine with and
without script.
>> but i don't understand how will u get rid of backup files in the permanent
>> directory from whatever u have mentioned, because gromacs creates the
output topology in the same location where it reads the input topology
from. so temperory directory thing will work only if u make an link of
top
>> file from permanent directory and use this linked version as input,
then
>> move the new top from temp to permanent directory.
>> bharat
>> On Fri, 11 May 2007, David Mobley wrote:
>>> All,
>>> I'm trying to write some wrappers to set up a project using standard
gromacs tools. Anyway, it looks to me like genbox is not handling its
path names correctly. In particular, here's what I did:
>>> - Make temporary directory in which to run genbox
>>> - Move to temporary directory, run genbox (reading input files from
permanent directory; writing input files to permanent directory) -
Change back to starting directory; delete temporary directory When I
do this, I get a blank output topology file in my permanent directory.
>>> It appears what's going on is that the file temp.top is written into
my temporary directory, but never moved into the permanent directory;
I suspect genbox is not handling the absolute/relative path issue
correctly here?
>>> I can work around, but this is just a bit annoying -- when I script
it, I end up with a bunch of "#temp.top.1#" etc files in my working
directory if I use editconf in the normal way, which is why I was
using the temporary directory thing to begin with.
>>> Thanks,
>>> David
>>> _______________________________________________
>>> gmx-users mailing list gmx-users at gromacs.org
>>> http://www.gromacs.org/mailman/listinfo/gmx-users
>>> Please search the archive at http://www.gromacs.org/search before
posting!
>>> Please don't post (un)subscribe requests to the list. Use the www
interface
>>> or send it to gmx-users-request at gromacs.org.
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>> ------------------------------
>> Message: 4
>> Date: Sat, 12 May 2007 11:13:00 +0200
>> From: David van der Spoel <spoel at xray.bmc.uu.se>
>> Subject: Re: [gmx-users] suggest small revision to genbox
>> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
>> Message-ID: <4645851C.2020301 at xray.bmc.uu.se>
>> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>> David Mobley wrote:
>>> All,
>>> I'm trying to write some wrappers to set up a project using standard
gromacs tools. Anyway, it looks to me like genbox is not handling its
path names correctly. In particular, here's what I did:
>>> - Make temporary directory in which to run genbox
>>> - Move to temporary directory, run genbox (reading input files from
permanent directory; writing input files to permanent directory) -
Change back to starting directory; delete temporary directory When I
do this, I get a blank output topology file in my permanent directory.
>>> It appears what's going on is that the file temp.top is written into
my temporary directory, but never moved into the permanent directory;
I suspect genbox is not handling the absolute/relative path issue
correctly here?
>>> I can work around, but this is just a bit annoying -- when I script
it, I end up with a bunch of "#temp.top.1#" etc files in my working
directory if I use editconf in the normal way, which is why I was
using the temporary directory thing to begin with.
>> Hi David,
>> plz submit a bugzilla with all input and scripts.
>> --
>> David.
>> ________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
>> Husargatan 3, Box 596, 75124 Uppsala, Sweden
>> phone: 46 18 471 4205 fax: 46 18 511 755
>> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++++
------------------------------
>> Message: 5
>> Date: Sat, 12 May 2007 14:03:11 +0530 (IST)
>> From: "Anil Kumar" <anil at chem.iitb.ac.in>
>> Subject: [gmx-users] Error while running MD in DMSO!
>> To: feenstra at few.vu.nl, gmx-users at gromacs.org
>> Message-ID: <33690.10.103.7.2.1178958791.squirrel at www.chem.iitb.ac.in>
Content-Type: text/plain;charset=iso-8859-1
>> Dear All,
>> I am running my simulations in explicit MeOH and DMSO. In case of MeOH, it
>> is running fine but while running in DMSO.
>> After running genbox i am having problem in running grompp for energy
minimization.
>> Error which i got is given below.
>> Cleaning up temporary file gromppkkHvWC
>> Fatal error: Atomtype 'SD' not found!
>> Please, anyone let me know why it is happening when i had used the
dmso.gro and dmso.itp files which is available by default to top
folder.
>> Thanks in advance.
>> With Warm Regards
>> Anil
>> --
>> (¨`•.•´¨) Always
>> `•.¸(¨`•.•´¨) Keep
>> (¨`•.•´¨)¸.•´ Smiling!
>> `•.¸.•´
>> «•´`•.(*•.¸(`•.¸ ¸.•´)¸.•*).•´`•»
>> «•´¨*•.¸¸. * ANIL *.¸¸.•*¨`•»
>> «•´`•.(¸.•´(¸.•* *•.¸)`•.¸).•´`•»
>> ANIL KUMAR(Research Scholar),
>> Bio-Organic Lab No-336(2nd Floor),
>> Dept. of Chemistry,I.I.T.Bombay,Powai,
>> Mumbai-400076,
>> Ph. No.-022-25764780(Lab)
>> -----------------------------------------
>> Residence:-
>> Hostel#1,Room#297,IIT Bombay,Powai,
>> Mumbai-400076,Ph.No.:-022-25721017(Hostel)
>> -------------------------------------------------
>> Web:http://chemanil.googlepages.com/
>> --------------------------
>> "Education is a progressive discovery of our ignorance"
>> - Will Durant
>> ----------------------------
>> ------------------------------
>> _______________________________________________
>> gmx-users mailing list
>> gmx-users at gromacs.org
>> http://www.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at http://www.gromacs.org/search before posting!
>> End of gmx-users Digest, Vol 37, Issue 44
>> *****************************************
>
>
>
>
>
> ------------------------------
>
> Message: 2
> Date: Sat, 12 May 2007 19:18:46 +0100 (BST)
> From: jagannath mondal <jmondal2004 at yahoo.co.in>
> Subject: RE: [gmx-users] problem with freeze-group : Large VCM(Berk
> Hess)
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <870979.95158.qm at web7904.mail.in.yahoo.com>
> Content-Type: text/plain; charset=iso-8859-1
>
> Hi Berk,
> Thanks a lot for your reply. According to your
> suggestion, I did not remove the cmm for the WHOLE
> molecule ---- i.e I used 'cmm-mode=None' for the
> entire system. (Did you mean that I should have
> removed the restriction only for freeze-group or for
> whole system?)
> But now I have two problems:
> 1) the simulation is now going for longer time but
> finally again crashes.
> 2) I freezed the mainchain because I did not want
> the mainchain
>
> move at all and I wanted the only side-chain move. But
> , when I am
>
> visualising the trajectory in VMD, I am finding that
> whole molecule is
>
>
> tumbling including the main-chain i.e the whole
> molecule is changing
>
> its position. As ususal, I did not use pressure
> coupling . Do you think that the movement of whole
> molecule is expected during freeze group simulation?
> should I modify something else in my parameter file?
> I am again giving the .mdp file.
> --- Berk Hess <gmx3 at hotmail.com> wrote:
>
>> >From: jagannath mondal <jmondal2004 at yahoo.co.in>
>> >Reply-To: Discussion list for GROMACS users
>> <gmx-users at gromacs.org>
>> >To: gmx-users at gromacs.org
>> >Subject: [gmx-users] problem with freeze-group :
>> Large VCM
>> >Date: Fri, 11 May 2007 00:19:53 +0100 (BST)
>> >
>> >Hi Gromacs user,
>> >
>> > I am a gromacs beginner struggling with
>> >freeze-group simulation.
>> > I was trying to simulate a
>> beta-peptide(un-natural
>> >peptide ) by relaxing only the side-chains but I am
>> >getting error regarding large VCM and
>> >The system has only 1 peptide (14-residue ) and No
>> >solvent. So, for this purpose , I generated a
>> >freeze-group which contains all the main-chain
>> atoms.
>> >Initially I was using pressure-coupling and it was
>> >giving error in simulation. Later I found many
>> >discussion on this freeze-group simulation in
>> >user-archive and manual and accordingly
>> > I did not use pressure-coupling in my simulation
>> >and before the simulation, I minimised my peptide
>> >using steep
>> > integrator and then with the minimised structure
>> I
>> >tried a MD run. But after 40 ps, the mdrun crashes
>> >with complaint about nsgrid and large VCM:
>> You should not remove com motion when using freeze
>> groups,
>> since the com is no longer free to move.
>> We should let grompp print a warning for this.
>> Berk.
> _________________________________________________________________
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>> gmx-users mailing list gmx-users at gromacs.org
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>> http://www.gromacs.org/search before posting!
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> ------------------------------
>
> Message: 3
> Date: Sun, 13 May 2007 09:12:01 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Error while running MD in DMSO!
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <464649C1.1050705 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Anil Kumar wrote:
>> Dear All,
>> I am running my simulations in explicit MeOH and DMSO. In case of MeOH, it
>> is running fine but while running in DMSO.
>> After running genbox i am having problem in running grompp for energy
minimization.
>> Error which i got is given below.
>> Cleaning up temporary file gromppkkHvWC
>> Fatal error: Atomtype 'SD' not found!
>> Please, anyone let me know why it is happening when i had used the
dmso.gro and dmso.itp files which is available by default to top
folder.
>
> They have to match the force field you're using, and the structure file
you're using.
>
> Mark
>
>
> ------------------------------
>
> Message: 4
> Date: Sun, 13 May 2007 09:16:15 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Error while running grompp for em (MD) in
> Urea
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <46464ABF.7000101 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Anil Kumar wrote:
>> Dear All,
>> Can anyone help me in running simulation in explicit urea.
>> When i was using urea+h2o.gro and urea.itp and tried to do simulation
in
>> explicit urea.
>> After doing genbox, i am not able to do the grompp for energy
>> minimization
>> and getting the error which is given below.
>> I have added masses of all the atoms of urea in atommass.dat file, but
still getting the same error.
>
> This file isn't used for making topologies.
>
>> Please help me, where does am i making the mistakes.
>> processing coordinates...
>> Warning: atom names in base.top and after_sol.gro don't match (OW -
OW1)
>> Warning: atom names in base.top and after_sol.gro don't match (HW1 - HW2)
>> Warning: atom names in base.top and after_sol.gro don't match (HW2 - HW3)
>
> Well, if these don't match you're doing something wrongly, but I can't
tell what.
>
>> double-checking input for internal consistency...
>> renumbering atomtypes...
>> converting bonded parameters...
>> # BONDS: 945
>> # G96BONDS: 128
>> # ANGLES: 1215
>> # G96ANGLES: 190
>> # PDIHS: 1134
>> # IDIHS: 485
>> # LJ14: 1242
>> # SETTLE: 2050
>> ERROR 4 [file "base.top", line 808]:
>> atom C1 (Res UREA-11) has mass 0
>> ERROR 5 [file "base.top", line 808]:
>> atom O2 (Res UREA-11) has mass 0
>> ERROR 6 [file "base.top", line 808]:
>> atom N3 (Res UREA-11) has mass 0
>> ERROR 7 [file "base.top", line 808]:
>> atom H4 (Res UREA-11) has mass 0
>> ERROR 8 [file "base.top", line 808]:
>> atom H5 (Res UREA-11) has mass 0
>> ERROR 9 [file "base.top", line 808]:
>> atom N6 (Res UREA-11) has mass 0
>> ERROR 10 [file "base.top", line 808]:
>> atom H7 (Res UREA-11) has mass 0
>
> Your force field's .rtp file needs entries for these atoms, probably.
>
> Mark
>
>
> ------------------------------
>
> Message: 5
> Date: Sun, 13 May 2007 09:23:26 +1000
> From: Mark Abraham <Mark.Abraham at anu.edu.au>
> Subject: Re: [gmx-users] Re: Parameterizing a force field (Mark
> Abraham)
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <46464C6E.6070409 at anu.edu.au>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Lee-Ping wrote:
>> Thank you both for the response! I looked at the -j option in mdrun,
but it looks like that has about as much documentation as ffscan (i.e.
none at all). I also fruitlessly checked the mailing list archives for
the past year and a half; there are some questions about ffscan, but
none of which contained instructions on how to run it.
>> The next step is to look inside the gromacs source code, but there are
a
>> lot of different files and I'm not sure as to which pieces of source
code describe how the input files are parsed. If you could tell me
which files to look at, I would appreciate it a lot. Thanks again!
>
> Mostly, files that parse files end in io.c
>
>> Specifically:
>> 1) What piece of code do I look at to see how mdrun parses the wham.gct
file (turned on by the -j switch)?
>
> Don't know. Start with src/kernel/mdrun.c and see what it calls to parse
this file.
>
>> 2) Which file describes how ffscan parses its inputs?
>
> Start with src/kernel/ffscan.c and see what it calls :-)
>
>> Also: If ffscan performs a grid scan, is it really able to fit 100+
parameters in a reasonable period of time (couple of hours)? Would a
numerical optimization procedure for the parameters be a possible
improvement over this?
>
> ffscan doesn't do a fit, per se, it just does a grid scan and reports
suitable values (see man ffscan). It'd have to be heaps faster than your
alternative scripts calling grompp and mdrun to do your series of single
point energy evaluations.
>
> Mark
>
>
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> End of gmx-users Digest, Vol 37, Issue 45
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