[gmx-users] pdb2gmx , or equivalent

[Justin Lemkul]

On 11/15/19 12:48 PM, Ling Chan wrote:
> Hello Colleagues,
>
> I would like to run Gromacs on some proteins that I have prepared. I see that you can obtain Gromacs input files using pdb2gmx. Just wonder if one can prevent pdb2gmx from tempering with your protein? I mean, pdb2gmx does a bunch of clean ups. I would like it to skip the clean up stage.
>
> I see that one can either let the clean up happen automatically, or have you tell it interactively whenever there is a decision to make. I would just like it to respect my structure – in the sense that no hydrogen is added or removed.

If you provide pdb2gmx with a structure that conforms to the force 
field's expectations of atom and residue naming, then pdb2gmx won't 
change anything about it.

-Justin

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================