Hello again,
I am trying to learn free energy calculations, however, it is much harder
than performing simple MD simulation. I would like to ask about
alchemistical calculation of mutating one ligand to another, especially
about vdw change step. When I mutated ligand1->ligand2 at lambda=0.25 a
got this result
http://postimg.org/image/adoq76m1r/
which shows some strange thing happening at a step of about 2000. So I
checked trajectory and this is what I see :
http://postimg.org/image/6ejpdhvub/
this image shows distance between ligand1 and ligand2. I am confused how
the DV/DL is beeing calculated and whether the calculation setup is right
- as clearly both ligands are interacting between each other.
I have used following setup:
icfe=1, clambda = 0.25,
ifsc=1,
timask1=':2', scmask1=':2',
timask2=':1', scmask2=':1',
crgmask=':1,2',
So my questions are following: What is the right way to calculate the vdw
change step? Is it ok to change whole ligands ( I am changing phenol to
serotonin for example)? Isn't it a problem - the result I got ?
Thank you very much for any advice!
Vlada
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Received on Thu Apr 23 2015 - 08:30:02 PDT
