Re: AMBER: [ A query]

From: Viktor Hornak <>
Date: Thu, 01 Mar 2007 13:56:40 -0500

Dear Ruchi,

David A. Case wrote:
> ----- Forwarded message from Ruchi Sachdeva <> -----
> From: Ruchi Sachdeva <>
> 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?
yes, this should be equivalent. So as you suggest, in amber8 leap you'd

source leaprc.ff99
loadamberparams frcmod.ff99SB

and it should be equivalent to issuing source leaprc.ff99SB in amber9.
You can check by comparing energies of the first step of dynamics with
topology file generated on your PC in amber9 and on the cluster with
amber8 using the procedure described before. If I remember well, the
topologies generated by amber8 and amber9 may be slightly different but
it shouldn't effect the energies (I think the only difference was in a
couple of terms which would have zero energies anyway).
> 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.
This should work and sounds actually easier than the previous approach.
Once you have the topology, amber8 should take it just fine.
> 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?
yes, the files should be compatible and both procedures should work.


> 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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Viktor Hornak
Center for Structural Biology   Phone: (631)632-1439
SUNY at Stony Brook             Fax:   (631)632-1555
Stony Brook, NY 11794-5115      E-mail:
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Received on Sun Mar 04 2007 - 06:07:43 PST
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