Hi Sergio,
The coefficients in the AMBER frcmod/parm files are not the Lennard-
Jones ACOEF and BCOEF, they are R_ii and epsilon_ii. (See here for
more: http://ambermd.org/Questions/vdwequation.pdf.) That issue
aside, these are still not the correct parameters for TIP3P. They
should be 1.7683 and 0.1520, respectively for the oxygen.
Best,
Paul
On May 9, 2011, at 10:04 AM, Wong, Sergio E. wrote:
> Dear Amber users;
>
> 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
>
> NOte that I changed the atom types from oh to oi and ho to hi.
> These do not match the published Lennard Jones 6-12 values for the
> TIP3P waters and I wonder where I went wrong. The published values
> are: 0.582 and 595 for the 6, 12 coefficents respectively. Any
> suggestions are greatly appreciated.
>
> Thank you;
>
> -Sergio
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Received on Mon May 09 2011 - 11:00:03 PDT
