[gmx-users] Negative arginine?

[Anton Feenstra]

Steven Spronk wrote:

> Sorry, I guess I didn't make myself very clear...
> 
> I have already performed a simulation with the (positive) arginine with a
> given electric field.  Now I want to run a simulation with the same
> electric field, but I'd like to see how a "negatively-charged" arginine
> would affect things differently.  This way the arginine would move the
> opposite direction in the same field.
> 
> Does anyone think that this technique would have any advantages over the
> mutation of the arginine to an acidic residue like glutamate?

If I understand correctly, you'd only want to reverse the direction of the 
force the arginine feels from the electric field, keeping all other things 
the same. And it seems many people agree that changing charges does not 
'keep all other things the same'.

Why not put a force directly on the arginine? IIRC, there is an option like 
'accelerate groups' in the mdp file, that adds an arbitrary acceleration (= 
force) in an arbitrary direction to an arbitrary group of atoms. If that 
group happens to be the Arg sidechain, and the force happens to be twice 
that generated by the electric field but in opposite direction, wouldn't 
that do exactly what you suggest, i.e. see what happens if the Arginine is 
pulled against the electric field?


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
|(   |   )| | | De Boelelaan 1083 - 1081 HV Amsterdam - Netherlands   |
| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/         |
|             | "If You See Me Getting High, Knock Me Down" (RHCP)    |
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