[gmx-users] adding SR2++ to charm27 force field
Ming Tang
m21.tang at qut.edu.au
Thu Apr 16 07:21:49 CEST 2015
Dear Mark and Justin,
Hi, Justin, I share the files in the dropbox to you. Thanks.
Here is the output:
tm at tm-HP-Z420-Workstation:~/bmp2$ grompp -f ions.mdp -c pb.pdb -p topol.top -o ions.tpr
GROMACS: gmx grompp, VERSION 5.0.4
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Sebastian Fritsch
Gerrit Groenhof Christoph Junghans Peter Kasson Carsten Kutzner
Per Larsson Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff
Erik Marklund Teemu Murtola Szilard Pall Sander Pronk
Roland Schulz Alexey Shvetsov Michael Shirts Alfons Sijbers
Peter Tieleman Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
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Copyright (c) 2001-2014, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out http://www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx grompp, VERSION 5.0.4
Executable: /your/installation/prefix/here/bin/gmx
Library dir: /your/installation/prefix/here/share/gromacs/top
Command line:
grompp -f ions.mdp -c pb.pdb -p topol.top -o ions.tpr
Setting the LD random seed to 3059859697
-------------------------------------------------------
Program grompp, VERSION 5.0.4
Source code file: /home/tm/Downloads/gromacs/src/gromacs/gmxpreprocess/toppush.c, line: 1019
Fatal error:
Atomtype SR not found
For more information and tips for troubleshooting, please check the GROMACS
website at http://www.gromacs.org/Documentation/Errors
-------------------------------------------------------
tm at tm-HP-Z420-Workstation:~/bmp2$
-----Original Message-----
From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of Mark Abraham
Sent: Thursday, 16 April 2015 1:50 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] adding SR2++ to charm27 force field
I asked to see the output. You can't be helped without someone seeing that.
Mark
On 15/04/2015 3:12 pm, "Ming Tang" <m21.tang at qut.edu.au> wrote:
> Hi Mark，
>
> pdb2gmx doesn't work， and it reminds the same error. Topol file was
> simply modified by mean from the topol file generated when considering
> MG2++
>
> Thanks
>
> Sent from my Huawei Mobile
>
> Mark Abraham <mark.j.abraham at gmail.com> wrote:
>
> Thanks. What is the whole pdb2gmx terminal output?
>
> Mark
>
> On Wed, Apr 15, 2015 at 3:05 AM, Ming Tang <m21.tang at qut.edu.au> wrote:
>
> > Dear Justin and mark,
> >
> > I modified the files like this:
> >
> > aminoacids.rtp
> >
> > [ MG ]
> > [ atoms ]
> > MG MG 2.00 0
> > [ SR ]
> > [ atoms ]
> > SR SR 2.00 0
> >
> > ions.itp
> >
> > [ moleculetype ]
> > ; molname nrexcl
> > MG 1
> >
> > [ atoms ]
> > ; id at type res nr residu name at name cg nr charge
> > 1 MG 1 MG MG 1 2
> >
> > [ moleculetype ]
> > ; molname nrexcl
> > SR 1
> >
> > [ atoms ]
> > ; id at type res nr residu name at name cg nr charge
> > 1 SR 1 SR SR 1 2
> >
> > ffnonbonded.itp
> >
> > CP1 MG 1 0.274842254546 0.051243325419
> > CP1 SR 1 0.310269 0.494658
> > whenever there is MG, I add SR.
> >
> > ffnanonbonded.itp
> >
> > CN7 MG 1 0.274842254546 0.051243325419
> > CN7 SR 1 0.310269 0.494658
> > whenever there is MG, I add SR.
> >
> > atomtypes.atp
> >
> > MG 24.305000 ; Magnesium Ion
> > SR 87.62000 ; Strontium Ion
> >
> > When I copy the modified force field to the working directory, the
> > PDB file used to consider MG Cannot be minimised too, which works
> > well with
> the
> > original Charmm27 force field. It reminds that atomtype SR not found
> again.
> > I use ready-made pdb file and topol file for minimization.
> >
> > thanks
> >
> > -----Original Message-----
> > From: gromacs.org_gmx-users-bounces at maillist.sys.kth.se [mailto:
> > gromacs.org_gmx-users-bounces at maillist.sys.kth.se] On Behalf Of
> > Justin Lemkul
> > Sent: Wednesday, 15 April 2015 1:22 AM
> > To: gmx-users at gromacs.org
> > Subject: Re: [gmx-users] adding SR2++ to charm27 force field
> >
> >
> >
> > On 4/14/15 5:12 AM, Ming Tang wrote:
> > > Hi Mark,
> > >
> > > Thanks for your reply. I am sure as I changed the files in the
> > charmm27.ff installed in my unbuntu system. Is there any other
> > things I need to consider?
> > >
> >
> > The files you listed are the only ones that should need to be modified.
> > Either you missed a step and think you did something you didn't, or
> > your changes didn't actually take effect (modifying the top-level
> > installation usually requires admin privileges, so if you tried to
> > modify without sudo or root it won't take).
> > Experiment with a local copy of the directory rather than
> > potentially messing up something system-wide. The error points most
> > likely to the
> .atp
> > file.
> >
> > -Justin
> >
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences School of Pharmacy Health
> > Sciences Facility II, Room 629 University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
> > --
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