On Fri, 2014-02-28 at 12:49 +0530, Arunima Shilpi wrote:
> Dear Sir
>
> I am studying the protein-ligand interaction by MMPBSA in xLeap.
> When the following command is executed it shows the following error
>
> saveAmberParm LIG lig.top lig.crd
>
> Fatal error: For atom .R<lig 1>.A<02 11>Could not find vdW (or other)
> parameter type: 0.3
This error message seems pretty straightforward. One of the atoms in
your ligand residue is assigned a type that is missing a set of
parameters.
>
> saveAmberParm receptor rec.top rec.crd
>
> Fatal error: Fatal Atom .R<LYS 948>.A<H2 24> does not have type.
Somehow one of the hydrogen atoms in your Lysine 948 residue was
assigned an atom name H2. There is no atom named H2 in the Lysine
residue according to the PDB standard (and the residue template
libraries that LEaP loads by default). You can either delete that atom
from the PDB and let tleap add the hydrogens automatically or you can
change that atom name to the one that tleap understands (you can find
the atom names in $AMBERHOME/dat/leap/lib/amino12.lib).
> How to debug these error.
I recommend working through the tutorials related to setting up custom
residues (
http://ambermd.org/tutorials/basic/tutorial4b/)
In the future when you are reporting problems, it helps to provide
details about your entire input (full input files and scripts you used).
In this case, it would help to know _every_ command you used in leap,
not just "saveAmberParm" since the mistake is often not in the command
that resulted in the error.
Good luck,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Fri Feb 28 2014 - 05:30:03 PST
