AMBER Archive (2007)

Subject: AMBER: [rsachdeva@imtech.res.in: A query]

From: David A. Case (case_at_scripps.edu)
Date: Thu Mar 01 2007 - 11:02:27 CST

----- Forwarded message from Ruchi Sachdeva <rsachdeva_at_imtech.res.in> -----

From: Ruchi Sachdeva <rsachdeva_at_imtech.res.in>
Date: Thu, 1 Mar 2007 19:59:36 +0530 (IST)
Subject: A query

I have one more query. I have AMBER9 installed on my local system (Linux,
single CPU) but our institute has the access to use supercomputing
facility i.e. HP cluster from other institute. There AMBER8 is installed.

Now I need to use ff99SB that is available with AMBER9. So I am thinking
of transfering frcmod.ff99SB file from my system to that cluster. Then I
would specify ff99 and then load frcmod99SB using xleap.

So I want to ask would this procedure be equivalent to use ff99SB directly?

Or else what can I do is to prepare prmtop and inpcrd files in my sytem
using AMBER9 and then transfer these files to the remote cluster.

Would these files be compatible with sander and other programs that are
provided with AMBER8 package since that cluster has AMBER8 installed?

Which of the above two procedures is right?

I would just like to mention here that this is just a temporary solution.
AMBER9 will be installed in the cluster but it will take some time.

Your help will be appreciated.

Thanks in advance

With Regards

Ruchi
Junior Research Fellow
Bioinformatics Center
Institute of Microbial Technology
Chandigarh, India

----- End forwarded message -----
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