AMBER Archive (2008)

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

From: Panwang Zhou (pwzhou_at_dicp.ac.cn)
Date: Thu Jun 19 2008 - 10:34:02 CDT

>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.



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


fox.gif

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" (in the *body* of the email)
      to majordomo_at_scripps.edu