Hi Mark Yeah i deleted it manually from the topology file and could able to progress further. But how could this happen.
So its better to file a report as you suggested. Thanks On Fri, Nov 14, 2014 at 4:50 PM, Mark Abraham <mark.j.abra...@gmail.com> wrote: > Hi, > > You seem to be suggesting that there is an entry in [bonds] that is 4800 to > 3368, and three others from that cysteine residue. That's highly > surprising, because this kind of workflow seems like something people > should have tried before... If so, then it would be good to file a report > at http://redmine.gromacs.org with your Gromacs version, input files and > pdb2gmx call, so that we can reproduce it and fix it. > > You can of course delete the lines with the spurious [bonds] entry. grompp > might complain if there are [angles] or [dihedrals] related to those, which > you could also delete. You should verify that the final > bonds+angles+dihedrals in the topology are what you think they should be. > > Mark > > On Fri, Nov 14, 2014 at 8:03 AM, Nixon Raj <nixn...@gmail.com> wrote: > > > Im dealing a protein with 4799 atoms and 1 ZN ion totally 4800 atoms. > > > > I need to form bonds between 4CYS-ZN , where i have equilibrium bond > > length, force constant and partial charges for the same fixed. > > > > Since i have new partial charge for Zn ion , i have created an ZN ion in > > name ZN1 . > > > > My specbond.dat is modified accordingly to add the necessary bonds , > > > > CYZ SG 1 ZN1 ZN 1 0.23 CYZ ZN1 > > > > Running the pdb2gmx yielded me > > > > Linking CYZ-210 SG-3368 and ZN1-299 ZN1-4800... > > > > Linking CYZ-260 SG-4195 and ZN1-299 ZN1-4800... > > > > Linking CYZ-263 SG-4250 and ZN1-299 ZN1-4800... > > > > Linking CYZ-270 SG-4358 and ZN1-299 ZN1-4800... > > > > Start terminus MET-1: NH3+ > > > > End terminus TYR-298: COO- > > > > Opening force field file ./charmm36.ff/merged.arn > > > > Checking for duplicate atoms.... > > > > Generating any missing hydrogen atoms and/or adding termini. > > > > Now there are 299 residues with 4800 atoms > > > > Making bonds... > > > > Number of bonds was 4859, now 4859 > > > > Generating angles, dihedrals and pairs... > > > > Before cleaning: 12729 pairs > > > > Before cleaning: 12834 dihedrals > > > > Keeping all generated dihedrals > > > > Making cmap torsions...There are 296 cmap torsion pairs > > > > There are 12834 dihedrals, 838 impropers, 8752 angles > > > > 12621 pairs, 4859 bonds and 0 virtual sites > > > > Total mass 34700.069 a.m.u. > > > > Total charge -8.000 e > > > > Writing topology > > > > But i could find 12 extra bonds created with ZN1(4800) in my topology > file. > > But the dihedrals and angles are in correct numbers. > > > > Each residue sharing 4 bonds with ZN1 (4800), i.e) CA-ZN1, HB1-ZN1, > HB2-ZN1 > > and SG-ZN1 , where i need only one bond i.e) SG-ZN1 with each cystein > > residue. > > > > Please help me to cross this roadblock. > > -- > > Gromacs Users mailing list > > > > * Please search the archive at > > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > > posting! > > > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > > > * For (un)subscribe requests visit > > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > > send a mail to gmx-users-requ...@gromacs.org. > > > -- > Gromacs Users mailing list > > * Please search the archive at > http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before > posting! > > * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists > > * For (un)subscribe requests visit > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or > send a mail to gmx-users-requ...@gromacs.org. > -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.