AMBER Archive (2002)

Subject: sander & prmtop file generated from antechamber input ?

From: jeff dyason (j.dyason_at_mailbox.gu.edu.au)
Date: Tue Apr 23 2002 - 22:33:58 CDT

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Hi,
        Using Amber 7 I was trying to go through the minimisation of a
small molecule as an introduction to working out how antechamber, leap
and sander work. When I went to run a sander job using the prmtop and
prmcrd files generated by leap from an antechamber generated file an
error appeared on the command line:-

bad atom type : ca

        This occurred using the prmtop & prmcrd files generated in the
antechamber test suite for the molecule sustiva. The sander job is, I
think, a simple minimisation and is as below :-

# Minimise cmpd1 with GB approx.
  &cntrl
     maxcyc=500, imin=1, cut=25.0, igb=1, ntb=0, ntpr=10, gbsa=1,
  &end

There are no errors reported in the mdout file. Looking at the prmtop
file the only place I can see any reference to "ca" is the following :-

%FLAG AMBER_ATOM_TYPE
%FORMAT(20a4)
ca ca ha ca cl ca ha ca ha ca n hn c o os c3 c3 f
f f
c1 c1 c3 hc c3 hc hc c3 hc hc

So, it looks like sander is not recognising the lower case atom types as
generated by antechamber.

Can anyone tell me what I have done wrong in setting up and running this
simple minimisation ?

Bye Jeff.
-----------
Jeff Dyason e-mail: J.Dyason_at_mailbox.gu.edu.au
Centre for Biomolecular Science and Drug Discovery
Griffith University (Gold Coast Campus)
        http://www.gu.edu.au/centre/cbsdd
PMB 50 Gold Coast Mail Centre Tel: +61 7 5552 7028
Queensland 9726 Australia Fax: +61 7 5552 8098

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