[gmx-users] Extra number of bonds created than specified (ZN-CYS)

[Mark Abraham]

On Fri, Nov 14, 2014 at 9:58 AM, Nixon Raj <nixnmtm at gmail.com> wrote:

> Hi Mark
>
> Yeah i deleted it manually from the topology file and could able to
> progress further. But how could this happen.
>

You really don't want to know ;-)


> So its better to file a report as you suggested. Thanks
>

Please do. That code is nearly impossible to reason about, so the actual
problem case is likely to be critical for fixing it.

Mark


> On Fri, Nov 14, 2014 at 4:50 PM, Mark Abraham <mark.j.abraham at 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 <nixnmtm at 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.
> > > --
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