Thank's,
A follow-up question:
Is it possible to freeze a set of atoms using NAB? (I could not find
this in ambertools 1.4 manual).
For example, by adding some lines to example given in amber tools
manual (listed below)?
This would be required when one uses procedure suggested by Kongsted
and Ryde (reference below).
terveisin Markus
(AmberTools1.4, page 283)
Here is a typical calling sequence:
molecule m; float x[4000], fret;
m = getpdb_prm( "mymolecule.pdb" );
mm_options( "cut=999., ntpr=50, nsnb=99999, diel=C, gb=1, dielc=1.0" );
mme_init( m, NULL, "::Z", x, NULL);
setxyz_from_mol( m, NULL, x );
// conjugate gradient minimization
conjgrad(x, 3*m.natoms, fret, mme, 0.1, 0.001, 2000 );
// Newton-Raphson minimization\fP
mm_options( "ntpr=1" );
newton( x, 3*m.natoms, fret, mme2, 0.00000001, 0.0, 6 );
// get the normal modes:
nmode( x, 3*m.natoms, mme2, 0, 0, 0.0, 0.0, 0);
.article{kongsted2009improved,
title={{An improved method to predict the entropy term with the
MM/PBSA approach}},
author={Kongsted, J. and Ryde, U.},
journal={Journal of computer-aided molecular design},
volume={23},
number={2},
pages={63--71},
issn={0920-654X},
year={2009},
publisher={Springer}
}
On 15 December 2010 15:21, case <case.biomaps.rutgers.edu> wrote:
> On Wed, Dec 15, 2010, Markus Kaukonen wrote:
>>
>> For testing purposes I'd like to calculate absolute entropy of a
>> single molecule in water using amber11.
>> Is this easily done by NAB or NMODE or ?
>
> You can do this in the rigid-rotor harmonic oscillator (RRHO) approximation.
> Either nmode or the nmode() function in NAB will provide this information.
>
> [Note that most water models used in biomolecular simulation are rigid models,
> and hence have no vibrational modes. nmode doesn't know this, and you would
> just have to ignore the vibrational contribution to the entropy.]
>
> ....dac
>
>
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>
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Received on Thu Dec 16 2010 - 00:30:02 PST
