[gmx-users] bypassing pdb2gmx

Tsjerk Wassenaar tsjerkw at gmail.com
Thu Sep 10 10:26:37 CEST 2009

Hi Amit,

You don't need to convert the .pdb file. Gromacs can handle several
file formats, including .pdb. If you have a topology that matches the
.pdb in terms of atoms, then you can simply proceed with the
subsequent steps.
pdb2gmx is not exactly meant to convert the structure file to another
file format, but to generate a topology for a system built up of well
defined blocks and, if necessary, edit the structure to match the
force field.



On Thu, Sep 10, 2009 at 2:29 AM, Amit Choubey <kgp.amit at gmail.com> wrote:
> hi everyone,
> I have a pdb file of my system and i want it to be fed into the GROMACS
> software. I have a new force field for the simulation and i have made the
> .top file manually which includes the new library FF files. I need to get a
> .gro file from the .pdb file that i have. So, is there a way out to do this
> without incorporating pdb2gmx because i dont use the standard FF and i dont
> really have all the other datafiles for the new FF except for necessary bond
> and nonbonded infos.
> Amit
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Tsjerk A. Wassenaar, Ph.D.
Junior UD (post-doc)
Biomolecular NMR, Bijvoet Center
Utrecht University
Padualaan 8
3584 CH Utrecht
The Netherlands
P: +31-30-2539931
F: +31-30-2537623

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