AMBER Archive (2007)

Subject: AMBER: RE: Problem loading pdf into tleap

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Wed Aug 08 2007 - 12:29:19 CDT

Dear Fatima,

Please post problems that are not directly related to the Amber tutorials to
the amber mailing list (amber_at_scripps.edu).

> Now, I have tried to load my own structure (pdb format) into
> leap (i m running
> tleap) but it did not work for some reasons:
> I attached the pdf file and listed here the leap.log file

> edi = loadpdb edicol_NHform.pdb
>...
> Created a new atom named: C1 within residue: .R<UNK 1>

Not realizing what is going on here means you don't really have an
understanding of the concept of classical force fields and parameter types.
The reason this is failing is because your molecule is not an amino acid or
DNA or other molecule that is part of the amber force field. Thus you need
to provide Leap with the necessary information regarding topology, atom
types, parameters etc. You also need to obtain charges and parameters. This
can be a very long winded process especially if you want to do it right...

As a first approximation you can attempt to use antechamber and the General
Amber force field (GAFF). This is fairly automated but is not a substitute
for due dilligence. Make sure you are well versed enough that you know how
to check the atom types and charges antechamber gives you and make sure you
know how to spot problems when they occur - Antechamber works pretty well
but doesn't always get atom types correct. If you are simulating thousands
of ligands the noise here might not be too much of a problem but if you are
going to spend many months running simulations of a single molecule then you
should probably parameterize this yourself. Start by doing a literature
survey for your system and similar systems to see if others have simulated
it before and how they did it.

I would also spend the time to read up on classical molecular dynamics. Read
the Amber 94 force field paper (Cornell, Et al JACS, 1995) - make sure you
understand it. Also read some text books on molecular dynamics and molecular
simulation.

The Antechamber tutorial is here:
http://amber.scripps.edu/tutorials/basic/tutorial4/index.htm

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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