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(
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html)
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 ?
http://www.gromacs.org/Documentation/Errors#Atom_X_in_residue_YYY_not_found_in_rtp_entry
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
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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