hi, heme group is not an amino acid, pdb2gmx only support the amino acids because .itp and .dat file in gromacs have only information about protein atoms not for other. so u just cut the co-ordinate of heme group from your pdb file save it in other pdb file and give input for Prodrg software it will return u co-ordinate of heme group in gromacs compatible format. u do pdb2gmx on only protein part and add both output file(pdb2gmx.gro and prodrg .gro)and proceed next step. u should read online John E. Kerrigan GROMACS Tutorial for Drug – Enzyme Complex. it will help u more. http://www2.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf
sanjay _______________________________________________ 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
