AMBER Archive (2008)

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

Date: Thu Jun 19 2008 - 09:47:50 CDT

Quoting Panwang Zhou <>:

> Hello, Amber users
> I'm trying to build a DMF solvent box using the gaff force filed. The
> initial solvent box was built using the xleap, then the MD studies were
> performed to equilibrate the solvent box. After equilibrium, the density of
> the solvent box was about 0.976 g/cc, which seems to be in accord with the
> experimental value (0.9445g/cc). The other properties I have not checked.
> Can anyone tell me how to extract the final solvent box from the obtained

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
> .rst or .mdcrd files? I want to obtain the "off" file which can be directly
> loaded by xleap.
>          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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