[gmx-users] Atom q2 not found in rtp database in residue TRP
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
>>gmx-users mailing list gmx-users at gromacs.org
>>Please don't post (un)subscribe requests to the list. Use the www interface
>>or send it to [EMAIL PROTECTED]
>>Can't post? Read http://www.gromacs.org/mailing_lists/users.php
>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
>gmx-users mailing list gmx-users at gromacs.org
More information about the gromacs.org_gmx-users