Hello, I am working with the simulation of cytochromeP450. There is a bond between the S of cystine and FE of HEME. During the grompp step I get warnings that there is no default bonds/angles/dihedrals all pertaining to the cystine-heme bond. In the archives it was mentioned that these values must be taken from ffG**bon.itp and included in the topology file. However in the ffG**bon.itp file, the bonds/angles mentioned seem to be between S of CYS and the carbon atom of HEME. For eg,
; bond-, angle- and dihedraltypes for specbonds: [ bondtypes ] S S 2 gb_33 NR FE 2 gb_32 ; cystine - heme link (is CR1-S, use CH2-S): S CR1 2 gb_30 Should not the cystine - heme link have FE insteadof CR1? I understand that I am missing some crucial point here. Kindly help. Thanks. Sarada Graduate student, NCBS, Bangalore _______________________________________________ gmx-users mailing list gmx-users@gromacs.org 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
