[gmx-users] error in topology file generation

[David van der Spoel]

Archana Chavan wrote:
> /hello everybody,/
> /i am new user to GROMACS,/
> /i want to perform simulations on docked protein ligand complex,/
> /During the conversion of the PDB file i came to such a problem:
> //just before the end  of conversion the program pdb2gmx.exe told that my
> //PDB file compound is not included into Gromacs residue topology database.
> //Directly as it says:
> //" Fatal error: Residue ''M_3' not found in residue topology database 
> "/ (which is docked ligand in the protein)
> /Woud you be so glad to tell me how can I resolve this problem? /
>  

chapter 5 in the manual.

> looking forward to your help
>  
> tahnks in advance.
>  
> 
> 
> -- 
> Archana Chavan
> MS (Pharm)Pharmacoinformatics
> National Institute of Pharmaceutical Education and Research (NIPER)
> Mohali-160 062
> Punjab, India.
> phone:+91-(0)-9888847223
> 
> 
> ------------------------------------------------------------------------
> 
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-- 
David.
________________________________________________________________________
David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  	75124 Uppsala, Sweden
phone:	46 18 471 4205		fax: 46 18 511 755
spoel at xray.bmc.uu.se	spoel at gromacs.org   http://folding.bmc.uu.se
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