[gmx-users] gromacs error

[Justin A. Lemkul]

pawan raghav wrote:
> I am using Gromacs on windows hen executing pdb2gmx command, I got an 
> error i.e.
>  
> Fatal error: Atom HD1 in residue HISB 3 not found in rtp entry with 14 
> atoms while sorting atoms. May be different protonation state. Remove 
> this hydrogen or choose a different protonation state.
>  
> I want to know what is the error type and where is rtp entry.
> 

Please read the manual.  Also, consult the following:

http://www.gromacs.org/Documentation/Errors#WARNING.3a_atom_X_is_missing_in_residue_XXX_Y_in_the_pdb_file

If you want more descriptive advice, provide us with your actual command line, 
snapshots of the .pdb file, etc.

-Justin

> -- 
> Pawan
> 

-- 
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Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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