[gmx-users] Re: gmx-users Digest, Vol 51, Issue 50
Justin A. Lemkul
jalemkul at vt.edu
Sun Jul 13 15:55:22 CEST 2008
Biswaranjan Meher wrote:
> 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 ?
Well, from what it shows here, your "input.pdb" file has only one frame, or at
least, only one frame with valid coordinates and box dimensions. I don't know
much about amb2gmx.pl, but I thought it's intent was to create a .top and .gro
from an AMBER-(xleap-)generated prmtop and inpcrd file. Please someone correct
me if I'm wrong.
Just recently, I developed my own shell script to convert an mdcrd to an .xtc
file, since a member of our lab need for some Gromacs analysis tools. Feel free
to download it from my site:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/scripts.html
The script has *not* been extensively tested, and I do not promise it will work,
but I am happy to try to help if problems arise. If bugs pop up, it will be
good to know to help make the script better :-)
-Justin
>
> 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
> <mailto: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
> <mailto:biswaranjan.meher at gmail.com>>
> Subject: [gmx-users] error in g_hbond
> To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> Message-ID:
> <b4c1302e0807120518p56d514cfpa98e69b521051c54 at mail.gmail.com
> <mailto: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 <mailto:nomadoro at gmail.com>>
> Subject: Re: [gmx-users] Can GROMACS mutate a residue?
> To: "Discussion list for GROMACS users" <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID:
> <e2838e4e0807120544t2d8c0858g1949a805131ba436 at mail.gmail.com
> <mailto: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
> <mailto: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
> <mailto: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
> <mailto: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
> <mailto: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 <http://vt.edu> | (540) 231-9080
> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > >
> > > ========================================
> > > _______________________________________________
> > > gmx-users mailing list gmx-users at gromacs.org
> <mailto: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
> <mailto: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
> <mailto: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
> <mailto:gmx-users-request at gromacs.org>.
> > Can't post? Read http://www.gromacs.org/mailing_lists/users.php
> >
>
>
>
> --
> 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 <mailto:jalemkul at vt.edu>>
> Subject: Re: [gmx-users] error in g_hbond
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <4878AD7C.8090504 at vt.edu <mailto: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
> <mailto: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
> <mailto: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 <http://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
> <mailto:sanni at theochem.uni-frankfurt.de>>
> Subject: [gmx-users] PME User
> To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> Message-ID: <200807121740.06885.sanni at theochem.uni-frankfurt.de
> <mailto: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/
> <http://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
> <mailto:spoel at xray.bmc.uu.se>>
> Subject: Re: [gmx-users] PME User
> To: Discussion list for GROMACS users <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> Message-ID: <4878D282.3050501 at xray.bmc.uu.se
> <mailto: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/
> <http://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
> <mailto: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
> <mailto: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 <mailto:spoel at xray.bmc.uu.se>
> spoel at gromacs.org <mailto: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 <mailto:prasun30 at gmail.com>>
> Subject: [gmx-users] gromacs bond type
> To: gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>
> Message-ID:
> <a473abdb0807122348v52f1dcfcw5b4241794eabb536 at mail.gmail.com
> <mailto: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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> posting!
>
> End of gmx-users Digest, Vol 51, Issue 50
> *****************************************
>
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
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--
========================================
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
========================================
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