AMBER Archive (2008)

Subject: AMBER: Questions on TIP4P model?

From: Chin, Keith B (keith.b.chin_at_jpl.nasa.gov)
Date: Fri Nov 28 2008 - 13:20:38 CST

Hi,

I'm performing MD with TIP4P model and have a few questions on amber *parmtop files

 1. In amber amber9/dat/solvents/tip4p dir, there is a parm.top file of tip4p water. The atomic mass of the extra point, EPW, is 3.0 instead of 0.0. For what purpose was the EPW point assigned a value of 3.0?
 2. There is also a pdb file, TIP4P_216.pdb, in the same directory containing partial charges in the last column; how was this pdb file created in xleap? When I used the savepdb cmd to create pdb file, it does not have correct partial charges in last column of file.
 3. Most importantly. In xleap, I created sand parmtop and parmcrd file using frcmod.tip4pew and frcmod.tip model files.
 For tip4pew model the partial charges in the parmtop file are:
                              O H1 H2 EPW
                  0.00000000E+00 9.55249411E+00 9.55249411E+00 -1.91049882E+01

              For tip4p model the partial charges in the parmtop file are:
O H1 H2 EPW
 0.00000000E+00 9.47559600E+00 9.47559600E+00 -1.89511920E+01

The partial charges for TIP4P should be 0.52 (H1 and H2) and -1.04 (EPW), respectively. Why are the parmtop partial charges so different? How are they computed?

Any info on these 3 issues would be greatly valuable to our research.

Thanks in advance.

-------------------------------------------------------
Keith Chin
Electrochemical Technologies Group
JPL/NASA
Office: (818) 354 - 4051

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