[gmx-users] bypassing pdb2gmx

[Justin A. Lemkul]

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.

-Justin

> Amit
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
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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
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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