Dear Amber User,
I want to do nmode analysis. I don't have
access of IMSL library. So, at first I minimized my protein in sander.
Then for nmdoe analysis I gave command like following:
$AMBERHOME/exe/nmode -O -i nmdin -o nmdout -p protein.prmtop -c
protein_min.rst -v vecs.
My nmdin file is like following:
normal mode analysis
&cntrl
ntrun = 1,
maxcyc = 0,
nvect = 12309,
ismem = 0,
ilevel = 6,
ivform = 1,
ntx = 1,
ntxo = 0
t = 300.00
/
But nmode is not running and showing a error like -
Root-mean-square gradient of input coords is 2.05278199572829
This is greater than the requested maximum: 1.000000000000000E-005
Do I have to increase drms value? Actually I don't want to minimize
the system. It is already minimized. I want to analyze nmode directly.
So what should I do? Please help..
sanjib
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Received on Wed Aug 29 2012 - 06:00:04 PDT
