Hi Gromacs Friends, Thank you mark for your solution . Sorry for my incomplete information on topic..
The CR atom type in ligand corresponds to the cyclohexane atoms in the ligands... I think I have to change the CR name , but what should be the new name???? With Best Wishes, David On Sat, Apr 21, 2012 at 6:27 PM, Mark Abraham <mark.abra...@anu.edu.au> wrote: > On 21/04/2012 9:27 PM, rama david wrote: >> >> 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 > > > The atomtype CR used in ligand .itp corresponds to no [atomtype] entry in > the standard force field, so grompp is stuck. You need to find out why > SwissParam thinks this is a reasonable atom type to use, and adapt your > solution accordingly. > > Mark > -- > 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 -- 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
