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 - 10:30:03 PDT
