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
[EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se
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