[MMTK] adding blocking groups and forcefields term

Konrad Hinsen research at khinsen.fastmail.net
Mon Feb 28 11:10:18 UTC 2011


On 21 Feb, 2011, at 18:39 , Osvaldo Martin wrote:

> I have a "couple" of questions (maybe "to naive" questions).
> 
> 1) How should I proceed in order to construct a protein from a PDB file and adding terminal blocking groups (like ACE and NME)

ACE and NME are treated like standard residues. For an example, have a look at the "bALA1" that is used in many of the examples. It's an alanine surrounded by ACE and NME.

> 2) It is possible to completely "turn off" electrostatic and/or VdW attractive energy terms? 

Everything is possible with MMTK - the question is just how much code you have to write yourself!

If you want to turn off one or the other term for the effect (not having the energies included), just set the corresponding cutoff to something very small (smaller than the shortest inter-atomic distance) but non-zero. This does leave a small CPU time overhead for the nonbonded list iteration. If you want to get rid of that as well, you need to write your own force field class and use it instead of Amber99ForceField. This is not as much effort as it may seem since Amber99ForceField is just a thin layer on top of MMForceField, which in turn is a very small class that combines the individual terms. To create your own variant, copy (and rename) MMForceField, then add the code from Amber99ForceField, and make the changes you want (such as replacing MMNonbondedForceField by MMLJForceField to remove electrostatics altogether).

> 3) MMTK support some-kind of implicit solvatation?

No, or perhaps better "not yet". Implicit solvent models should be easy to integrate into MMTK's force field system, but all the code remains to be written.

Konrad.
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Konrad Hinsen
Centre de Biophysique Moléculaire, CNRS Orléans
Synchrotron Soleil - Division Expériences
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E-Mail: research AT khinsen DOT fastmail DOT net
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