[AMBER] problems in nmode and -use-mdins option (MMPBSA.py)

From: houcemeddine <hothman.pasteur.fr>
Date: Tue, 24 Dec 2013 16:55:12 +0100

Hi everybody,
I run some tests for MMPBSA.py to estimate the free energy using GB, and
Nmode for a protein-protein complex (nearly 5500 atom) in order to rank
some docking poses.
Using maxcyc=10 and 20 runs the calculation simultaniously for 15 and
30 min for only one snapshot. I am aware that the entropy term is
computationaly expensive, however in my case it seems that the
calculation converges very slowly while my estimations of computation
time is 10 days/snapshot
Does someone have any idea about this issue?

I also desired to use an input file to tune the parameters for Nmode
with -use-mdins flag. The issue is that only the _MMPBSA_gb.mdin is
generated at the end of the calculation but not
_MMPBSA_sander_nm_min.mdin neither _MMPBSA_nmode.in were present even if
I use the -make-mdins flag. is there any explanation for this ?

My MMPBSA script file:

input file for running PB and GB



best regards

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Received on Tue Dec 24 2013 - 08:00:02 PST
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