Hi,
I realized that the protein structure was the problem.
After building the missing residues (schrodinger prime module) prmtop and
inpcrd were generated without errors.
The charge command on the unit gives a value of 0.005998. This is after
neutralizing with 3 Cl- ions.
Do you consider this value of charge negligible or this needs further
adjustment?
Thank you.
Cheers.
Vaibhav
On Thu, Apr 9, 2015 at 1:00 PM, David A Case <case.biomaps.rutgers.edu>
wrote:
> On Thu, Apr 09, 2015, Vaibhav Dixit wrote:
>
> > But I am getting strange warnings from tleap that there are large bonds
> > between atoms of the same residues (protein and ligand).
> > I have checked the coordinates for a couple of them and this doesn't look
> > to be the case.
>
> > WARNING: There is a bond of 20.901524 angstroms between:
> > ------- .R<CYS 58>.A<CB 5> and .R<CYS 58>.A<SG 8>
>
> In addition to Jason's point about perhaps needing TER cards, note that
> many
> of the warnings are about bonds between side-chain atoms in the same
> residue.
>
> This is very unusal. Can you say exactly what you did to "check the
> coordinates"? Be sure that the coordinates in the input pdb file are in
> the correct columns (PDB format is column-specific). Try loading just a
> small
> piece of the protein (e.g. just residues 58-59) to see if that helps to
> debug
> the problem. Use ambpdb or savepdb to create a pdb file from Amber prmtop,
> and examine that visually (i.e. the otuput pdb, *not* your input pdb file).
>
> These are just suggestions. Learning how to debug problems with
> simulations
> is a key task, since problems are sure to arise from time to time.
>
> ....dac
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
With Regards.
Dr. Vaibhav A. Dixit,
Postdoctoral Research Scientist,
Etherow F40/6,
AstraZeneca,
Charter Way,
Silk Road Business Park,
Macclesfield,
Cheshire,
England,
SK10 2NX
Ext. No. 20278
Email: Vaibhav.Dixit.astrazeneca.com
Moblie Number: +44-7448233157, +91-7709129400.
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
Please consider the environment before printing this e-mail
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Apr 09 2015 - 07:30:05 PDT
