Re: [AMBER] Parameter bond and angle file could not find

From: Jason Swails <jason.swails.gmail.com>
Date: Wed, 24 Sep 2014 10:26:39 -0400

On Wed, Sep 24, 2014 at 9:39 AM, Vishal Nemaysh <
vishal.bioinfotech.gmail.com> wrote:

> *Dear all, I am getting a error leap when i prepare the .top and .crd
> files. How to resolve it? the pdb file and final pdb file is also attached
> herewith. Thanks in advance*
>
>
> *> loadamberparams frcmod.ionsjc_tip3p*
> Loading parameters:
> /home/vnemaysh/Desktop/AMBER12/amber12/dat/leap/parm/frcmod.ionsjc_tip3p
> Reading force field modification type file (frcmod)
> Reading title:
> Monovalent ion parameters for Ewald and TIP3P water from Joung & Cheatham
> JPCB (2008)
> *> saveamberparm 1YCC 1YCC.top 1YCC.crd*
> Checking Unit.
> WARNING: There is a bond of 5.722328 angstroms between:
> ------- .R<CYS 14>.A<SG 8> and .R<CYS 17>.A<SG 8>
> WARNING: There is a bond of 5.722328 angstroms between:
> ------- .R<CYS 14>.A<SG 8> and .R<CYS 17>.A<SG 8>
>

‚ÄčThere seems to be a disulfide bond defined between residues 14 and 17.
Any cystine that is involved in a disulfide bond has to be renamed CYX in
the PDB file.

I suggest downloading and installing AmberTools 14 and looking at the
"pdb4amber" tool that is released there. That tool is designed to help
prepare PDB files for use with Amber, and will make these kinds of common
changes as well as make other suggestions that you may not think about.

HTH,
Jason
‚Äč
-- 
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed Sep 24 2014 - 07:30:02 PDT
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