AMBER: Parallelizin antechamber?

From: Francesco Pietra <>
Date: Tue, 14 Aug 2007 06:29:11 -0700 (PDT)

I wonder whether there may be other users also wishing that antechamber is
parallelized in the future.

I have already used successfully antechamber/gaff with a number of
non-polymeric molecules, up to 100 atoms per molecule. Found difficult groups
for antechamber, thouugh overcome. Now a big step: 5oo atoms, non polymeric.
Furnished to antechamber minimized with a molecular mechanics package as a pdb
file. Could not carry out a global space search because of too many variables
(1500) for the MM package.

AM1 is minimizing since 26 hours, now at cycle 404, while E is still decreasing
by -0.15 kcal/mol per step, for a total 5% decrease of E (160 kcal/mole) since
the beginning. DELTAX oscillating between 0.001 and 0.002. Of course I wish I
had a parallelized minimizer.

What makes me very curious is the temperature setting for the minimization,
1000 K. To overcome barriers? I was totally unaware of that possibility, if
this is the case, for a conformational search through electronic calculations.

A surprise was the -nc flag able to introduce the electrons lacking after that
certain atoms (such as of sulfate ester groups) came to antechamber through a
pdb file, thus having lost the parameterization of the MM package, thus coming
as electron unpaired. The overall negative charge was reestablished though the
-nc flag. This was a problem I was wondering how to surmount, until I hopeless
tried -nc and the surprise came. Previously, I had tried unsuccessfully to
inform antechamber of the negative charge at specific oxygen atoms (identified
through VMD) by setting "-1" at columns 79-80 of pdb.


francesco pietra

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Received on Wed Aug 15 2007 - 06:07:48 PDT
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