Hi,
You can freeze atoms in nab using mme_init. Instead of passing NULL
as the 2nd arg pass in a string representing all atoms you want to
move (e.g. ":11,12" for residues 11 and 12). All other atoms will be
frozen.
-Dan
On Thursday, December 16, 2010, Markus Kaukonen <markus.kaukonen.iki.fi> wrote:
> 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
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> --www=http://www.iki.fi/markus.kaukonen
> --Markus.Kaukonen.iki.fi
> --office: N102 Nano building FIN-02015 TKK
> --home: Viinirinne 3 F 12, 02630 Espoo, FIN
> --tel: h 045-1242068, w 4518694, 050-5112785
> --Rikos ei kannata, eika maatalous
> --Suomessa. (Paimio 1998) ---
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
-------------------------
Daniel R. Roe
Postdoctoral Associate
SAS - Chemistry & Chemical Biology
610 Taylor Road
Piscataway, NJ 08854
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Dec 16 2010 - 05:00:02 PST
