AMBER Archive (2008)

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

From: Panwang Zhou (
Date: Thu Jun 19 2008 - 09:13:18 CDT

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 .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


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