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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