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

Nixon Raj nixnmtm at gmail.com
Fri Nov 14 08:03:20 CET 2014

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

Please help me to cross this roadblock.

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