[gmx-users] Re: gmx-users Digest, Vol 51, Issue 50
Biswaranjan Meher
biswaranjan.meher at gmail.com
Sun Jul 13 15:30:01 CEST 2008
Hello Justin.
Nice to hear from you.
I did the conversion of AMBER files to GROMACS type by the amb2gmx.pl found
in the ffAMBER tools.
I used the command:
g_hbond -f input.pdb -s topol.tpr -n index.ndx -num hbnum.xvg -hbn
hbond.ndx -hbm hbmap.xpm -r 0.4
My input was a pdb file generated from the AMBER trajectory (mdcrd).
I checked the .gro file (onverted from AMBER) with gmxcheck, of which output
is here I am pasting. Just have a look.
Checking file notty.gro
Reading frames from gro file 'notty.gro created by rdparm2gmx.pl Fri Jul 11
17:38:48 IST 2008', 30261 atoms.
Reading frame 0 time 0.000
# Atoms 30261
Precision 0.001 (nm)
Last frame 0 time 0.000
Item #frames Timestep (ps)
Step 0
Time 0
Lambda 0
Coords 1
Velocities 0
Forces 0
Box 1
Can you please suggest , what may be the possible error from this ?
BRM
gcq#254: "O My God, They Killed Kenny !" (South Park)
On Sun, Jul 13, 2008 at 12:19 PM, <gmx-users-request at gromacs.org> wrote:
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> Today's Topics:
>
> 1. error in g_hbond (Biswaranjan Meher)
> 2. Re: Can GROMACS mutate a residue? (Lee Soin)
> 3. Re: error in g_hbond (Justin A. Lemkul)
> 4. PME User (Sang-Min Park)
> 5. Re: PME User (David van der Spoel)
> 6. gromacs bond type (prasun kumar)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Sat, 12 Jul 2008 17:48:04 +0530
> From: "Biswaranjan Meher" <biswaranjan.meher at gmail.com>
> Subject: [gmx-users] error in g_hbond
> To: gmx-users at gromacs.org
> Message-ID:
> <b4c1302e0807120518p56d514cfpa98e69b521051c54 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Dear GROMACS users,
> I am new to gmx-users.
>
> I am analysing the H-bonding in my trajectory with the tool g_hbond.
> The trajectory was generated by the AMBER force fields.
> Now I have converted the AMBER prmtop and inpcrd files to GROMACS .top and
> .gro files.
>
> When I performed the g_hbond, I encountered with a fatal error
>
> Your computational box has shrunk too much.
> g_hbond can not handle this situation, sorry.
>
> Also I checked the postings in the archive related to this problem, but I
> didnt get the solution completely.
> So is it a problem of my AMBER traj./pdb files I am using or it some thing
> else.
> Can anyone will help me in this regard to get the solution ?
>
> Thanks in advance for your kind suggestions.
>
> BRM
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> ------------------------------
>
> Message: 2
> Date: Sat, 12 Jul 2008 20:44:45 +0800
> From: "Lee Soin" <nomadoro at gmail.com>
> Subject: Re: [gmx-users] Can GROMACS mutate a residue?
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org>
> Message-ID:
> <e2838e4e0807120544t2d8c0858g1949a805131ba436 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> Thanks! And I've learned that Pymol can also do the job.
>
> 2008/7/12 DEEPESH AGARWAL <deepesh.iitd at gmail.com>:
>
> > Hi,
> >
> > In addition to what Justin has suggested, VMD has a tool to mutate a
> > residue- Extensions>Modeling>Mutate residue.
> >
> > Deepesh
> >
> >
> > On 7/12/08, Justin A. Lemkul <jalemkul at vt.edu> wrote:
> > >
> > >
> > > Lee Soin wrote:
> > >> Hi!
> > >> Is there a command in GROMACS that can substitute the atoms of a whole
> > >> residue for another? This is quite useful in doing mutation
> simulations.
> > >> Or if that's not possible, how should I mutate a residue? Thanks!
> > >
> > > I would use a program like DeepView (Swiss-PDBViewer), or maybe
> Modeller.
> > >
> > > -Justin
> > >
> > >>
> > >> --
> > >> Sun Li
> > >> Department of Physics
> > >> Nanjing University, China
> > >>
> > >>
> > >>
> ------------------------------------------------------------------------
> > >>
> > >> _______________________________________________
> > >> 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
> > >
> > > --
> > > ========================================
> > >
> > > Justin A. Lemkul
> > > Graduate Research Assistant
> > > Department of Biochemistry
> > > Virginia Tech
> > > Blacksburg, VA
> > > jalemkul[at]vt.edu | (540) 231-9080
> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > >
> > > ========================================
> > > _______________________________________________
> > > 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
> > >
> > _______________________________________________
> > 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!
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> >
>
>
>
> --
> Sun Li
> Department of Physics
> Nanjing University, China
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> ------------------------------
>
> Message: 3
> Date: Sat, 12 Jul 2008 09:11:24 -0400
> From: "Justin A. Lemkul" <jalemkul at vt.edu>
> Subject: Re: [gmx-users] error in g_hbond
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4878AD7C.8090504 at vt.edu>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
>
>
> Biswaranjan Meher wrote:
> > Dear GROMACS users,
> > I am new to gmx-users.
> >
> > I am analysing the H-bonding in my trajectory with the tool g_hbond.
> > The trajectory was generated by the AMBER force fields.
> > Now I have converted the AMBER prmtop and inpcrd files to GROMACS .top
> > and .gro files.
>
> How did you do this conversion?
>
> >
> > When I performed the g_hbond, I encountered with a fatal error
>
> What was the command you issued? Were you analyzing the .gro file, or some
> converted mdcrd file?
>
> >
> > Your computational box has shrunk too much.
> > g_hbond can not handle this situation, sorry.
> >
> > Also I checked the postings in the archive related to this problem, but
> > I didnt get the solution completely.
> > So is it a problem of my AMBER traj./pdb files I am using or it some
> > thing else.
> > Can anyone will help me in this regard to get the solution ?
>
> Use gmxcheck on whatever files you have tried to analyze to see if they
> contain
> the appropriate box vectors. I don't know how you did the conversion of
> the
> files from AMBER --> GROMACS, so that's a possible source of error.
>
> -Justin
>
> >
> > Thanks in advance for your kind suggestions.
> >
> > BRM
> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
> > 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
>
> --
> ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------
>
> Message: 4
> Date: Sat, 12 Jul 2008 17:40:06 +0200
> From: Sang-Min Park <sanni at theochem.uni-frankfurt.de>
> Subject: [gmx-users] PME User
> To: gmx-users at gromacs.org
> Message-ID: <200807121740.06885.sanni at theochem.uni-frankfurt.de>
> Content-Type: text/plain; charset="iso-8859-1"
>
>
> Dear all,
>
> I read in www.gromacs.org/gromacs/revisions/ in the report of
> David van der Spoel
>
> "Added support for a combination of PME and User determined coulomb
> potentials. The user has to take care that the combination of Coulomb and
> standard PME makes sense" ( 8 Feb. 2005)
>
> I don't understand what that means.
>
> As I know the Ewald Sum consist of the reciprocal and direct space term
> which are derivated for the f(x)=1/r function.
>
> In this sense I don't know what gromacs would do when I would specify
> PME-User with a potential that is different from f(x).
>
> 1. Can someone explain me what gromacs is doing when one sets PME-User ?
>
>
> 2. Furthermore I would like to know if the user defined potential tables
> are
> also used to calculate the long range interactions.
>
> Thank you for your time
>
>
> ------------------------------
>
> Message: 5
> Date: Sat, 12 Jul 2008 17:49:22 +0200
> From: David van der Spoel <spoel at xray.bmc.uu.se>
> Subject: Re: [gmx-users] PME User
> To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> Message-ID: <4878D282.3050501 at xray.bmc.uu.se>
> Content-Type: text/plain; charset=ISO-8859-1; format=flowed
>
> Sang-Min Park wrote:
> > Dear all,
> >
> > I read in www.gromacs.org/gromacs/revisions/ in the report of
> > David van der Spoel
> >
> > "Added support for a combination of PME and User determined coulomb
> > potentials. The user has to take care that the combination of Coulomb
> and
> > standard PME makes sense" ( 8 Feb. 2005)
> >
> > I don't understand what that means.
> >
> > As I know the Ewald Sum consist of the reciprocal and direct space term
> > which are derivated for the f(x)=1/r function.
> >
> > In this sense I don't know what gromacs would do when I would specify
> > PME-User with a potential that is different from f(x).
> >
> > 1. Can someone explain me what gromacs is doing when one sets PME-User ?
>
> Let's say you want to replace the Coulomb potential Fc(r) by your own
> Fuser(r). Then you have to subtract the Long Range part of the coulomb
> potential Fc(r,LR) from your F(r) in the short range potential to get
> the correct sum. Note that this also dependent on the cut-off, so if you
> decide to change the cut-off you need a new lookup table for the
> short-range.
>
> >
> > 2. Furthermore I would like to know if the user defined potential tables
> are
> > also used to calculate the long range interactions.
> >
> > Thank you for your time
> > _______________________________________________
> > 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
>
>
> --
> David van der Spoel, Ph.D., Professor of Biology
> Molec. Biophys. group, Dept. of Cell & Molec. Biol., Uppsala University.
> Box 596, 75124 Uppsala, Sweden. Phone: +46184714205. Fax: +4618511755.
> spoel at xray.bmc.uu.se spoel at gromacs.org http://folding.bmc.uu.se
>
>
> ------------------------------
>
> Message: 6
> Date: Sun, 13 Jul 2008 12:18:41 +0530
> From: "prasun kumar" <prasun30 at gmail.com>
> Subject: [gmx-users] gromacs bond type
> To: gmx-users at gromacs.org
> Message-ID:
> <a473abdb0807122348v52f1dcfcw5b4241794eabb536 at mail.gmail.com>
> Content-Type: text/plain; charset="iso-8859-1"
>
> dear users,
> I am trying to get some information about the bond type,angle type and
> dihedral angle type.
> can any one please tell me what is the bond type of C-F.angle type for
> F-C-F,dihedral angle type of F-C-C-O &F-C-C-H.
> Or any one can tell me how to define the gromacs type for bonds,angles.I
> tried to read the 5th chapter but not getting any thing.
> actually i am lookig forward to include TFE in the rtp file for my
> simulation of peptide in TFE.
> Please help me.
> Thanx in advance
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> End of gmx-users Digest, Vol 51, Issue 50
> *****************************************
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