AMBER Archive (2006)

Subject: Re: AMBER: prepi definitions

From: ivan_at_mmb.pcb.ub.es
Date: Wed Feb 01 2006 - 10:33:42 CST


Hi Mike !!

zeros mean no database generation and "2" means a force field with all
atom model

more detailed info:

http://amber.scripps.edu/formats.html

Hope this helps,

best regards

Ivan

On Wed, 1 Feb 2006, Michael Mazanetz wrote:

> Dear AMBER forum,
>
> I am interested in understanding the format of the prepi file as depicted below:
>
> 0 0 2
>
> This is a remark line
> molecule.res
> SUS INT 0
> CORRECT OMIT DU BEG
> 0.0000
> 1 DUMM DU M 0 -1 -2 0.000 .0 .0 .00000
> 2 DUMM DU M 1 0 -1 1.449 .0 .0 .00000
> 3 DUMM DU M 2 1 0 1.522 111.1 .0 .00000
> 4 C2 ca M 3 2 1 1.540 111.208 180.000 -0.17826
> 5 C1 ca M 4 3 2 1.386 86.897 -162.979 -0.04968
> 6 H1 ha E 5 4 3 1.072 120.119 25.599 0.16937
> 7 C14 ca M 5 4 3 1.379 119.724 -154.668 -0.01913
>
> etc
>
> What does the first line 0 0 2 mean? Where can I find more information about this and other file types?
>
> Regards,
>
> Mike
>
>
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-- 
   _______________________________________________
 /                                                 \
/   Ivan Marchan Carvajal                           \
|   (PhD Student)                                   |
|                                                   |
|   Institut de Recerca Biomedica de Barcelona      |
|   Parc Cientific de Barcelona                     |
|   Molecular Modelling & Bionformatics Group       |
|   http://mmb.pcb.ub.es                            |
|                                                   |
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