Hello, I am working with the simulation of cytochromeP450. In the output of the pdb2gmx command, the iron atom in the HEME loses all the bonds, including the sulphide bond with cystine. Also, the command changed the residue name from HEME to HEC. During the execution of the pdb2gmx, I get this warning:
Warning: 'HEC' not found in residue topology database, trying to use 'HEME' Can someone please tell me, if this is responsible for the loss of bonds especially the one between CYS and FE. How can the bonds be retained? Thanks. Sarada _______________________________________________ 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
