Re: [AMBER] Zinc parameterization

From: Jason Swails <>
Date: Fri, 1 Aug 2014 18:15:03 -0400

On Fri, Aug 1, 2014 at 5:54 PM, Pengfei Li <>

> Hi Nadia,
> In AMBER FF the Cys group which has S-S linkage with another Cys
> group has a residue name as CYX, which is different from CYS and CYM,
> Another two Cys groups in AMBER FF. I guess the problem is about the
> residue name in pdb file but not sure.
> Jason, can leap automatically assign the S-S bond to Cys residues which
> has a CYS residue name in pdb file but has two S atoms are close to each
> other?

The only bonds that tleap adds are:

1) Bonds defined in residue library files
2) Bonds defined by PDB CONECT records
3) Bonds you add with the "bond" command

If you use "pdb4amber", that program may automatically add disulfide bonds


Jason M. Swails
Rutgers University
Postdoctoral Researcher
AMBER mailing list
Received on Fri Aug 01 2014 - 15:30:02 PDT
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