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
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Received on Thu Apr 09 2015 - 05:30:02 PDT
