[gmx-users] protein topology file fetal error
jalemkul at vt.edu
Sat Jan 26 14:18:52 CET 2013
On 1/26/13 4:41 AM, az kalsom wrote:
> hi all,
> i am new to gromacs, when i run my protein file by following the tutorial
> example mention here(
> I AM GETTING THE FOLLOWING ERROR FOR MY PROTEIN PDB FILE..
> Fatal error:
> Atom HA in residue SER 705 was not found in rtp entry SER with 10 atoms
> while sorting atoms.*
> PLEASE HELP ME IN REMOVING THIS ERROR
> WHAT SHOULD I DO TO REMOVE THIS ERROR ?
You haven't said exactly what you're dealing with, but if you're trying to use a
united-atom force field as in my tutorial, these force fields do not have
explicit nonpolar hydrogen atoms. Adding -ignh to pdb2gmx is probably the solution.
Justin A. Lemkul, Ph.D.
Department of Biochemistry
jalemkul[at]vt.edu | (540) 231-9080
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