AMBER Archive (2008)

Subject: Re: Re: AMBER: How to extract solvent box information from .rst or .mdcrd files?

From: fatima.chami_at_durham.ac.uk
Date: Thu Jun 19 2008 - 11:00:32 CDT

Quoting Panwang Zhou <pwzhou_at_dicp.ac.cn>:

> >Quoting fatima.chami <fatima.chami_at_durham.ac.uk>:
>
> >
> >the box information is printed in the last line of .rst or mdcrd
> >you should read x y z and three angles (for example just tail :)
> >74.6826000 73.3782000 73.8666000 90.0000000 90.0000000 90.0000000
> >
> >best wishes
> >fATIMA
>
> Thanks for your replay. Actually I'm wondering how to creat the ".off" file
> of the equilibriumed solvent box based on the obtained .rst or .mdcrd file. I
> can extract the PDB file of the final solvent box, but it cann't be loader
> correctly by the xleap when using the gaff force filed, as the atom types in
> the obtained PDB file is not the same with those used in the gaff force
> field.
how did you generate your topology files in the first place before running your
simulation.
If you have used any prepin or frcmod files you should load them again into
Leap to be able to read your pdb

hope this helps
Fatima

>
>
>
> 　　　　　　　　 Panwang Zhou
> 　　　　　　　　 Dalian Institute of Chemical Physics
> Chinese Academy of Sciences.
> Tel: 0411-84379195 Fax: 0411-84675584
> 2008-06-19
>
> 

-- 
Dr. F.Chami
Science Lab.
Department of Chemistry
Durham University
South Road Durham, DH 1 4 LE
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