[gmx-users] Re: bypassing pdb2gmx

Amit Choubey kgp.amit at gmail.com
Thu Sep 10 02:40:46 CEST 2009

hi everyone,
I guess if i knew the exact format of .gro files i could write a small code
to copy data from pdb to gro . I cannot find this info anywhere. I believe
that it has co-ordinates and velocities but how are the velocities choose
(randomly?). I am also not sure abt the exact order.


On Wed, Sep 9, 2009 at 5:29 PM, 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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