Hi all,
I would like to test a patch made to Ambertools1.5 for decomposed MMPBSA
calculations, which would also require sander in Amber11. So I compiled
Ambertools1.5 under my home directory.
In order to use amber11(on the cluster)/bin/sander, but to use
amber11(self-compiled)/bin/MMPBSA,
I followed Jason's instructions on "Installing Ambertools 12 and Older
Amber" (
http://jswails.wikidot.com/installing-ambertools-12-and-older-amber),
just replace Ambertools12 by the self-compiled Ambertoos1.5. These are what
I did:
export AMBERHOME=/home/user/amber11
export PATH=$PATH:=/home/user/amber11/bin:/directory on cluster for
amber/amber11/bin
The problem is that when I type `which MMPBSA`, it still calls MMPBSA from
amber11 on the cluster, in spite that AMBERHOME was set to
/home/user/amber11.
And if I ran calculation by using the full path to MMPBSA as
/home/user/amber11/bin/MMPBSA -y 1.mdcrd -cp complex.top -lp lig.top -rp
rec.top -i mmpbsa.in , the program will stop and say "Error: sander could
not be found!", although if I type `which sander`, it calls /directory on
cluster for amber/amber11/bin/sander
Could you please advise on how to appropriately use self compiled
Ambertools1.5 and Amber11 on the cluster?
Thanks!
Qiong
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Received on Tue May 22 2012 - 08:00:04 PDT
