[gmx-users] energy minimization

Justin Lemkul jalemkul at vt.edu
Sun Jul 15 14:52:55 CEST 2018

On 7/15/18 1:38 AM, farial tavakoli wrote:
>   Dear Justin
> But I copied & pasted topolgen and perl5 folders in the working directory. and faced the mentioned error.
> Can't open perl script "topolgen.pl": No such file or directory
> I dont know how I should figure out this problem.

The problem is still the same: there's nothing called "topolgen.pl" in 
the working directory. List your files, you'll see it's called something 

> Which one of all-atom force fields will you choose to run a simulation on a complex with small molecule, if you want to calculate binding energy using G_MMPBSA ?I really need your guidance .

Presumably any of them, but I don't do such calculations.



Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129


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