Re: [AMBER] ligand topology genaration

From: Jason Swails <jason.swails.gmail.com>
Date: Tue, 12 Jan 2016 07:28:02 -0500

On Tue, Jan 12, 2016 at 6:35 AM, neha chaudhary <nehachaudhary769.gmail.com>
wrote:

> Hello Sir,
>
> I saved topology files for ligand successfully but in case of protein I am
> getting the following error. I used the commands as :
>
> >source leaprc.ff99SB
> >saveAmberParm receptor rec.top rec.crd
> Checking Unit.
> WARNING: The unperturbed charge of the unit: -3.000000 is not zero.
>
> -- ignoring the warning.
>
> Building topology.
> Building atom parameters.
> Building bond parameters.
> Could not find bond parameter for: SH - SH
> Could not find bond parameter for: SH - SH
> Could not find bond parameter for: SH - SH
> Could not find bond parameter for: SH - SH
> Could not find bond parameter for: SH - SH
>

‚ÄčThis is what happens when leap tries to add a disulfide bond between two
cysteine residues AND tries to add a hydrogen atom to the end of the
cysteine side-chain. You can't do both.

Any cysteine residues involved in a disulfide bridge needs to be renamed to
CYX inside the PDB file. The program "pdb4amber" will automatically do
this for you, so I suggest taking your original PDB file and using
"pdb4amber" on it to get it properly prepared to run through tleap.

HTH,
Jason

-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Tue Jan 12 2016 - 04:30:02 PST
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