On Wed, Aug 06, 2014, Hirdesh Kumar wrote:
> I am trying to prepare the ATP molecule (attached) using antechamber. I
> added hydrogen using xleap and the used antechamber to prepare it..
>
> With following commands:
> *antechamber -i ATP_H.pdb -fi pdb -o ATP_H.ac -fo ac -c bcc -nc -4*
>
> I got this error:
> *Running: /opt/bwgrid/chem/amber/12/bin/sqm -O -i sqm.in <http://sqm.in> -o
> sqm.out*
> *Error: cannot run "/opt/bwgrid/chem/amber/12/bin/sqm -O -i sqm.in
> <http://sqm.in> -o sqm.out" of bcc() in charge.c properly, exit...*
As the sqm.out file shows, the program failed to acheive self-consistency,
which can often be a problem with highly charged anions. You might try the
suggestions in Note 6 on p. 262 of the Amber manual.
A better suggestion is to use the ATP parameters available here:
http://www.pharmacy.manchester.ac.uk/bryce/amber
(Look under "cofactors"; input files and references to the original papers are
provided.)
....dac
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Received on Wed Aug 06 2014 - 09:30:02 PDT
