See the "-nc" command line option for antechamber.
E.g. (The following should work. Although you should check the QM output
carefully to be sure)
antechamber -i g98.out -fi gout -o sustiva_resp.mol2 -fo mol2 -c resp -nc 3
All the best
Ross
/\
\/
|\oss Walker
| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- ross.rosswalker.co.uk |
|
http://www.rosswalker.co.uk <
http://www.rosswalker.co.uk/> | PGP Key
available on request |
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From: owner-amber.scripps.edu [mailto:owner-amber.scripps.edu] On Behalf Of
priya priya
Sent: Monday, October 16, 2006 00:01
To: amber.scripps.edu
Subject: AMBER: Amber8: problem related to antechamber
Dear All
When I use antechamber to load a peptoid sequence
(peptoids have the amino acid side chain appended to
amide nitrogen ratther then alpha carbon) containing
charged residues (like lysine). it says "ODD NUMBER OF
ELECTRONS"....Check!
There are three lysine residues and the total number of electrons come out
to be 834 but antechamber is taking 837 number of electrons (not considering
the +3 charge of the three lysine residues.
Please suggest how to make the prepin file of such charged residues..
Sincerely
Priya Anand
_____
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Received on Wed Oct 18 2006 - 06:07:16 PDT
