AMBER Archive (2008)

Subject: Re: AMBER: from Gromax to AMBER

From: Cristina Sisu (csds2_at_cam.ac.uk)
Date: Tue May 13 2008 - 08:49:12 CDT

Great,

I'll try that. Fingers crossed!

Cristina

jacopo.sgrignani_at_unifi.it wrote:
> 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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