[gmx-users] protein topology file fetal error

[Justin Lemkul]

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

-- 
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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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