RE: AMBER: Problem about prepare the model when running antechamber

From: Ross Walker <>
Date: Mon, 4 Jun 2007 13:47:24 -0700


> I ran antechamber to parameterize my molecule consists of 1125 atoms.

This is way beyond the capabilities of antechamber and even if you could
modify it to work your chances of obtaining a decent set of charges and
parameters is close to nil. You should read up on the RESP method for
calculating charges so that you are familiar with it and more importantly
with it's limitations. Such grid based methods never do well with buried
atoms and in your case with 1125 atoms I suspect a large number of them are
buried and so will likely be assigned non-realistic charges. Add to this the
fact that you need to run QM calculations on this entire system and you
should start to see the problem.

I strongly urge you to search the literature for previous work on collagen
models, then look at carefully parameterizing this system, including
breaking it down into manageable (and meaningful) chunks and then manually
assigning atom types and developing suitable parameters yourself.
This will require a considerable amount of effort but unfortunately there is
no magic bullet in this field.

Good luck.

|\oss Walker

| HPC Consultant and Staff Scientist |
| San Diego Supercomputer Center |
| Tel: +1 858 822 0854 | EMail:- |
| | PGP Key available on request |

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Received on Wed Jun 06 2007 - 06:07:22 PDT
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