[gmx-users] -ignh command removes protonation site of interest
jalemkul at vt.edu
Tue Apr 16 01:06:06 CEST 2019
On 4/15/19 6:30 PM, Neena Susan Eappen wrote:
> Hello gromacs users,
> I started with a peptide where protonation site was on a carbonyl oxygen. However, using -ignh command in pdb2gmx, I lose that proton from there. Any insights on how to move forward?
If you want another protonation state, then you need to make sure the
residue is named as expected by the force field (e.g. ASPP for
protonated aspartate, not ASP, etc).
Justin A. Lemkul, Ph.D.
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
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