On Mon, May 09, 2011, Wong, Sergio E. wrote:
>
> I am trying to perform a TI calculations where I decouple a
> water molecule. For this, I created a dummy water mocule. To
> obtain all the relevant force field parameters, I took a water
> residue ("WAT") from a pdb file created by amber, ran it thruogh
> antechamber to get a template *.prepi file, modified the charges
> so they are consistent with the TIP3P model and went on to use
> parmchk to make a *.frcmod file. I am using AMBER 10.
>
> The problem is that the nonbonded (Lennard Jones parameters) seem odd. I get :
>
>
> NONBON
> oi 1.7210 0.2104
> hi 0.0000 0.0000
Antechamber creates parameters using the GAFF force field; this is not
necessarily the same as TIP3P. You can either (a) load solvents.lib [which is
automatically loaded with most leaprc files] and use its "TP3" residue, or
(b) hand-edit your frcmod file to use the LJ values appropriate to the oxygen
in TIP3P water.
You really should do the former, since Amber adds an H-H bond to TIP3P to keep
it rigid (via SHAKE). I don't think the default antechamber procedure would
do that.
Finally, we have occasionally encountered problems in decoupling water
molecules, and haven't been able to track down the problem. So, be alert to
any funny business. [Maybe InSuk can elaborate here.]
....dac
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Received on Mon May 09 2011 - 11:00:05 PDT
