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

Joern Lenz JLenz at zbh.uni-hamburg.de
Mon Nov 6 15:15:56 CET 2006

>>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.

I checked both suggestions but the error is still there.
what can i further do to run pdb2gmx correctly ?
thnaks a lot for ideas.

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