AMBER Archive (2008)

Subject: RE: AMBER: from Gromax to AMBER

From: jacopo.sgrignani_at_unifi.it
Date: Tue May 13 2008 - 08:19:19 CDT

Dear Cristina,
I'm using gromacs trajectories to perform MM-PBSA and I usually process
my file with this procedure:

I import the prmtop file of the system in VMD, after I import the
gromacs xtc file as trajectory and I save a mdrcd (with box) using
exoport coordinates.
This is usually a good procedure.

Sometime I had same problem whit the ligand receptor and complex
topologies for MM-PBSA but maybe I was for my error, in the topology
preparation.

Ciao

Jacopo

>Dear Ambers,
>
>I have problems running Amber on multiple nodes on our cluster. This has
>nothing to do with Amber, as my computer officer assured me, but with
>some environment modules. However gromax dose not have the same problem.
>Now, I need to do some MM-PBSA calculations on my proteins. My question
>is, can I run a production run with gromax and then use the trajectory
>file obtained there for the mm-pbsa calculations?
>
>Is there a way to inter-convert the files of the two systems?
>
>Thanks,
>
>Cristina
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