[gmx-users] bypassing pdb2gmx

Justin A. Lemkul jalemkul at vt.edu
Thu Sep 10 02:57:03 CEST 2009

Amit Choubey 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.

You don't actually need a .gro to do anything; all Gromacs tools function just 
fine with .pdb format.  If you really want a .gro, use editconf.


> Amit
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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