[gmx-users] Atom q2 not found in rtp database in residue TRP

[David van der Spoel]

Joern Lenz wrote:
> dear gromacs users,
> 
> i am performing a simulation of a system of a protein together with a DNA 
> using the amber03 forcefield which i loaded down from  
> http://folding.stanford.edu/AMBER.html.
> I converted all LYS residues in my pdb file into LYP and all HIS into HIP 
> (please correct me if you think that this does not make sense).
> Does anyone know a script or program which automatically converts pdb files 
> into amber pdb files so that i can use the amber03 FF without changing atoms 
> here and there ?
> 
> QUESTION: 
> When i start pdb2gmx there always occurs the same error:
> "Atom q2 not found in rtp database in residue TRP"
> I cannot recognize where this error comes from and so i am not able to fix 
> this error.
> Has anyone got an idea ? 

check that the columns in your pdb file are correct.
search for q2 in your pdb file.

> Thanks a lot and have a nice day using gromacs
> greeting 
> joern
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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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