On Wed, Jan 15, 2014 at 9:17 AM, Zhuang, Yu <yu.zhuang.tum.de> wrote:
> Dear Amber users,
>
> Currently I am doing the pre-treatment of protein model by Xleap. However,
> there is an error occurs as following. Did anyone knows how I could solve
> this problem? I would like to generate a prmtop and inpcrd file for Amber.
> Many many thanks in advance.
>
> > saveamberparm unit 2q2m_wat.prmtop 2q2m_wat.inpcrd
> Checking Unit.
> WARNING: The unperturbed charge of the unit: -0.999887 is not zero.
>
> -- ignoring the warning.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Could not find bond parameter for: SH - SH
> Building angle parameters.
> Could not find angle parameter: HS - SH - SH
> Could not find angle parameter: SH - SH - C2
> Could not find angle parameter: SH - SH - HS
> Could not find angle parameter: C2 - SH - SH
> Building proper torsion parameters.
> ** No torsion terms for HS-SH-SH-C2
> ** No torsion terms for HS-SH-SH-HS
> ** No torsion terms for C2-SH-SH-C2
> ** No torsion terms for C2-SH-SH-HS
>
It looks like you tried to form disulfide bonds between two CYS residues.
For tleap, the PDB file has to be modified so that cysteine residues
involved in disulfide bonds are named CYX instead of CYS.
See section 4.4 of the AmberTools manual for more instructions regarding
system setup with tleap (subsection 4.4.2 has instructions for proteins,
for instance).
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Jan 15 2014 - 08:30:03 PST
