Hi Mark, I have been experiencing a similar thing. I found that there is no specific entry for the amber force fields in tip4p.itp file, so I guess that gromacs was then using the default one, which has different atom types. For me, gromacs is in /usr/local/gromacs, so I went to /usr/local/gromacs/share/gromacs/top, where I found tip4p.itp. I edited [ atoms ] section in this file from:
[ atoms ] ; id at type res nr residu name at name cg nr charge #ifdef _FF_OPLS 1 opls_113 1 SOL OW 1 0.0 2 opls_114 1 SOL HW1 1 0.52 3 opls_114 1 SOL HW2 1 0.52 4 opls_115 1 SOL MW 1 -1.04 #else #ifdef _FF_GROMOS96 1 OWT4 1 SOL OW 1 0.0 15.9994 2 H 1 SOL HW1 1 0.52 1.008 3 H 1 SOL HW2 1 0.52 1.008 4 IW 1 SOL MW 1 -1.04 0.0 #else 1 OWT4 1 SOL OW 1 0.0 2 HW 1 SOL HW1 1 0.52 3 HW 1 SOL HW2 1 0.52 4 IW 1 SOL MW 1 -1.04 #endif #endif to: [ atoms ] ; id at type res nr residu name at name cg nr charge #ifdef _FF_OPLS 1 opls_113 1 SOL OW 1 0.0 2 opls_114 1 SOL HW1 1 0.52 3 opls_114 1 SOL HW2 1 0.52 4 opls_115 1 SOL MW 1 -1.04 #else #ifdef _FF_GROMOS96 1 OWT4 1 SOL OW 1 0.0 15.9994 2 H 1 SOL HW1 1 0.52 1.008 3 H 1 SOL HW2 1 0.52 1.008 4 IW 1 SOL MW 1 -1.04 0.0 #else #ifdef _FF_AMBER99 1 amber99_61 1 SOL OW 1 0.0 15.9994 2 amber99_60 1 SOL HW2 1 0.52 1.008 3 amber99_60 1 SOL HW3 1 0.52 1.008 4 MW 1 SOL MW4 1 -1.04 0.0 #else 1 OWT4 1 SOL OW 1 0.0 2 HW 1 SOL HW1 1 0.52 3 HW 1 SOL HW2 1 0.52 4 IW 1 SOL MW 1 -1.04 #endif #endif #endif i.e. added in a section that tells gromacs what to do in the case of an amber force field. I found this out by looking at the file ffamber_tip4EW.itp, to see what atom types gromacs was expecting. I hope that helps :-) Kevin -- Kevin Channon School of Chemistry University of Bristol UK -- Kevin Channon School of Chemistry University of Bristol UK _______________________________________________ gmx-users mailing list [email protected] http://www.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search before posting! 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
