AMBER Archive (2006)

Subject: Re: AMBER: How to build 1,4-dimethyl benzene with amber9

From: martin peters (peters_at_ufl.edu)
Date: Fri Apr 28 2006 - 18:00:29 CDT

Hi All,

I understood that the sequence command constructed the new unit from
the internal coordinates of the fragments.
Am I mistaken believing it should at least reproduce the geometry
from the prep file for each fragment,
though it may get the inter-fragment conformation wrong?

I would like to be able to create a fragment library, similar to that
of glycam, for drug-type molecules.
The 1,4-dimethyl benzene test is just a proof of concept.

Cheers,

Martin.

Martin B. Peters
Graduate Student, Merz Group
Department of Chemistry
Quantum Theory Project
2240 New Physics Building
PO Box 118435
University of Florida
Gainesville, Florida 32611-8436

On Apr 28, 2006, at 6:10 PM, Ross Walker wrote:

> Hi Martin,
>
>> source leaprc.ff94
>> gaff = loadamberparams gaff.dat
>> loadamberprep PSB.prepin
>> loadamberprep CH3.prepin
>> mol = sequence { CH3 PSB }
>
> This is the problem here. The sequence command just builds
> structures using
> common templates it doesn't have any idea of ring planarity, stereo
> chemistry etc.
>
> You have two options here. The first option is not to worry about the
> initial structure. Just try minimising the system and see if the
> structure
> corrects itself. It probably will. if it doesn't you can try do
> some short
> low temperature MD with a short time step (say 0.2fs) and then cool
> the
> system down to 0 K. This will work where minimisation may fail
> since it will
> allow you to move out of what is potentially a high energy minimum.
>
> The second option is to build the starting structure outside of
> leap and
> load in a pdb into leap instead of using the sequence command. I.e.
> you
> could run a simple MM2 calculation or a small QM calculation on the
> system
> and then convert the output file into a pdb. Then edit this pdb.
> Give the
> various atoms their correct residue ids and then do:
>
> loadamberprep PSB.prepin
> loadamberprep CH3.prepin
> mol = loadpdb my_molecule.pdb
>
> This should then retain the structure from the pdb file rather than
> those
> from the prepin file.
>
> good luck...
>
> Ross
>
> /\
> \/
> |\oss Walker
>
> | HPC Consultant and Staff Scientist |
> | San Diego Supercomputer Center |
> | Tel: +1 858 822 0854 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk | PGP Key available on request |
>
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