On Wed, Aug 29, 2012 at 11:03 AM, David A Case <case.biomaps.rutgers.edu>wrote:
> 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.)
>
To add on a little here, scee and scnb, in particular, are different
between the two programs, last I checked. I would also echo Dave's
sentiments about using the nmode() function in NAB to do normal mode
analysis.
There is an example of how to use it that Dwight McGee wrote at
$AMBERHOME/AmberTools/src/mmpbsa_py/mmpbsa_entropy.nab that shows a sample
program using that call (and it also performs a minimization beforehand).
You can also use MMPBSA.py directly to do nmode calculations on an entire
trajectory (you can submit a single PDB file or restart file to MMPBSA.py
with the -y flag to calculate only a single trajectory). If you specify
only a complex topology file, then it will perform calculations on a single
system (i.e., it doesn't *only* do binding free energy calculations).
HTH,
Jason
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Aug 29 2012 - 08:30:04 PDT
