[AMBER] MMPBSA calculation for chlorine anion

From: zhihong ke <ebelleke.gmail.com>
Date: Wed, 8 Dec 2010 12:25:19 -0700

Dear All:

Has anyone done any MMPBSA calculation for chlorine anion with MMPBSA.py?
Since the parameter for surface area for Cl- is missing in mdread.f in
sander package.
I add this line to this file:
            else if (atype == 'IM' .or. atype == 'Cl-') then
               x(L165-1+i) = 1.70d0 + 1.4d0
which lead to a NaN vdW interaction energy.

On the other hand, I defined a new atom type for Cl- as Cl by mistake.
And the same parameter was assigned to Cl.
Then I could get a reasonable vdW interaction energy.

The sole difference between these two calculation is the atom type.
For the "Cl", the mdread.f would read is as "C" since it starts with C,
and the surface parameter for C is :
     else if (atype(1:1) == 'C' .or. atype(1:1) == 'c') then
               x(L165-1+i) = 1.70d0 + 1.4d0,
exactly the same as for IM.
However, that leads to a totally different result.

Do I miss something?

Any help would be greatly appreciated!

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Received on Wed Dec 08 2010 - 11:30:03 PST
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