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

[Mark Abraham]

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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