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

[Joern Lenz]

>>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.
Joern

>>Thanks a lot and have a nice day using gromacs
>>
>>greetings 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
>[EMAIL PROTECTED]       [EMAIL PROTECTED]   http://folding.bmc.uu.se
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