AMBER Archive (2008)

Subject: Re: AMBER: Questions on TIP4P model?

From: Carlos Simmerling (carlos.simmerling_at_gmail.com)
Date: Fri Nov 28 2008 - 14:03:14 CST

partial charges in the prmtop files are not in electron units. check
the amber web page FAQ and file formats description.
also, pdb files normally don't contain partial charges- you need to
specify that you want them (such as with ptraj's -pqr option)

On Fri, Nov 28, 2008 at 2:20 PM, Chin, Keith B
<keith.b.chin_at_jpl.nasa.gov> wrote:
> Hi,
>
>
>
> I'm performing MD with TIP4P model and have a few questions on amber
> *parmtop files
>
>
>
> 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?
> 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.
> 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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