Re: [AMBER] problem to perform nmode analysis

From: David A Case <>
Date: Wed, 29 Aug 2012 11:03:32 -0400

On Wed, Aug 29, 2012, Sanjib Paul wrote:

> 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.

No, it is not already minimized, at least as far as nmode is concerned.
You should carefully compare the energies printed out at the end of the sander
run with those printed by nmode. There is probably some difference (which
could be caused by having different defaults in the two programs.) You have
to make sure that the energy function is the same in the two programs (or, use
nmode for both minimization and normal mode calculation.)

Unless this is just a one-off calculation (i.e. the last normal mode
calculation you plan to do), I'd advise getting AmberTools and using the
nmode() function in NAB. That makes it much easier to minimize the energy
and to get the modes in a single run.


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Received on Wed Aug 29 2012 - 08:30:03 PDT
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