Hi Gromacs Friends, I wish to apply charmff 27 to my protein and ligand I proceed in following way ..
1. I separate the protein and ligand by grep command then delete the ligand lne grom pdb file 2 I generate the topology of protein in gromacs using the pdb2gmx command 3 I generate the ligand topology by swissparam , 4 I protein top , I added the line.. ; Include ligand topology #include "ligand.itp" The ligand.itp generated by swissparam contain position restrain file in it Ligand itp has following line..... 1 CR 1 LIG C1 1 0.0000 12.0110 2 CR 1 LIG C2 2 0.0000 12.0110 3 CR 1 LIG C3 3 0.0000 12.0110 4 CR 1 LIG C4 4 0.0000 12.0110 5 CR 1 LIG C5 5 0.0000 12.0110 6 CR 1 LIG C6 6 0.0000 12.0110 7 CR 1 LIG CM 7 0.5030 12.0110 8 NRP 1 LIG N 8 -0.8530 14.0067 9 HNRP 1 LIG HN1 9 0.4500 1.0079 10 HNRP 1 LIG HN2 10 0.4500 1.0079 11 HNRP 1 LIG HN3 11 0.4500 1.0079 12 HCMM 1 LIG H1 12 0.0000 1.0079 13 HCMM 1 LIG H22 13 0.0000 1.0079 14 HCMM 1 LIG H23 14 0.0000 1.0079 15 HCMM 1 LIG H32 15 0.0000 1.0079 16 HCMM 1 LIG H33 16 0.0000 1.0079 17 HCMM 1 LIG H42 17 0.0000 1.0079 18 HCMM 1 LIG H43 18 0.0000 1.0079 19 HCMM 1 LIG H52 19 0.0000 1.0079 20 HCMM 1 LIG H53 20 0.0000 1.0079 21 HCMM 1 LIG H62 21 0.0000 1.0079 22 HCMM 1 LIG H63 22 0.0000 1.0079 23 HCMM 1 LIG HM2 23 0.0000 1.0079 24 HCMM 1 LIG HM3 24 0.0000 1.0079 . . . Now when I give the grompp command I stuck with following error ... Program grompp, VERSION 4.5.4 Source code file: /build/buildd/gromacs-4.5.4/src/kernel/toppush.c, line: 1166 Fatal error: Atomtype CR not found How to solve the error.. All suggestion are welcome.. Thank you in Advance... Have a good day.!!! With Best Wishes, Rama David. -- gmx-users mailing list gmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/Search before posting! Please don't post (un)subscribe requests to the list. Use the www interface or send it to gmx-users-requ...@gromacs.org. Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
