[gmx-users] free energy perturbation

[Anton Feenstra]

emathe at gmu.edu wrote:
> Hello,
> I am attempting to introduce a mutation (I->L) in a small protein (87 
> residues) via free energy perturbation.  I get a strange resulting 
> structure, mainly the leucine that I should obtain does not resemble a 
> leucine (it looks like a hybrid between I and L).  The following shows 
> my mdp options and the changes I made to the topology file.  Thanks for 
> any help,
[...]

You only list changes in the [atoms] section of your .top file, is
that correct? If so, that explains your problem: you will also have
to modify bonds, angles and dihedrals settinge. And, this is not
trivial as the connectivity of your molecule changes. That means that
bonds, angles, dihedrals (and an improper) will have to appear and
disappear accordingly. It can probably be done, but if you don't do
it right you can expect strange or even wrong results.


-- 
Groetjes,

Anton
  _____________ _______________________________________________________
|             |                                                       |
|  _   _  ___,| K. Anton Feenstra                                     |
| / \ / \'| | | Dept. of Pharmacochem. - Vrije Universiteit Amsterdam |
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| \_/ \_/ | | | Tel: +31 20 44 47608 - Fax: +31 20 44 47610           |
|             | Feenstra at chem.vu.nl - www.chem.vu.nl/~feenstra/       |
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