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 ? Thanks a lot and have a nice day using gromacs greeting 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
