>>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 >>_______________________________________________ >>gmx-users mailing list [email protected] >>http://www.gromacs.org/mailman/listinfo/gmx-users >> >>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. >________________________________________________________________________ >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 [email protected] >http://www.gromacs.org/mailman/listinfo/gmx-users _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users 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
