[AMBER] Parameter bond and angle file could not find

From: Vishal Nemaysh <vishal.bioinfotech.gmail.com>
Date: Wed, 24 Sep 2014 19:09:27 +0530

*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>

 -- ignoring the warnings.

Building topology.
Building atom parameters.
Building bond parameters.
Could not find bond parameter for: SH - SH
Could not find bond parameter for: SH - SH
Building angle parameters.
Could not find angle parameter: HS - SH - SH
Could not find angle parameter: HS - SH - SH
Could not find angle parameter: SH - SH - 2C
Could not find angle parameter: SH - SH - HS
Could not find angle parameter: SH - SH - 2C
Could not find angle parameter: SH - SH - HS
Could not find angle parameter: 2C - SH - SH
Could not find angle parameter: 2C - SH - SH
Building proper torsion parameters.

-- 
Vishal
Research Scholar,
Neuropharmaceutical Chemistry lab.,
Dr. B. R. Ambedkar Center for Biomedical Research,
University of Delhi, Delhi-110007
Email: *vishal.bioinfotech.gmail.com <vishal.bioinfotech.gmail.com>*
Phone: 91-11-27662778 Mobile: 91+9650736653




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Received on Wed Sep 24 2014 - 07:00:02 PDT
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