# Re: [AMBER] MM-PBSA atom types

From: bharat lakhani <lakhbharat.gmail.com>
Date: Mon, 3 Aug 2015 18:50:47 -0400

Not yet I am still trying to figure out what those lines means If i have to
add for O3 atomtype and where to get those values?

else if (atype == 'O2') then
x(l165-1+i) = 1.60d0 + 1.4d0
x(l170-1+i) = 0.88857d0
x(l175-1+i) = -0.33421d0
x(l180-1+i) = -0.0018683d0
x(l185-1+i) = 0.00049372d0

On Mon, Aug 3, 2015 at 6:37 PM, Jason Swails <jason.swails.gmail.com> wrote:

> Did you recompile Amber after you made that change?
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
>
> > On Aug 3, 2015, at 6:24 PM, bharat lakhani <lakhbharat.gmail.com> wrote:
> >
> > Dear Amber Users
> >
> > I am getting following error on running MM-PBSA calculation. After
> reading
> > previous threads I have to add in
> > ~/amber14/AmberTools/src/sander/mdread2.F90. But i am just confused what
> > else need to be added
> >
> > Beginning GB calculations with ~/amber14/bin/sander
> > calculating complex contribution...
> > bad atom type: O3
> >
> >
> > But i am just confused on what is needed here for atomtype O3
> >
> > else if (atomicnumber .eq. 8) then
> > if (atype == 'O ') then
> > x(l165-1+i) = 1.60d0 + 1.4d0
> > x(l170-1+i) = 0.68563d0
> > x(l175-1+i) = -0.1868d0
> > x(l180-1+i) = -0.00135573d0
> > x(l185-1+i) = 0.00023743d0
> > else if (atype == 'O2') then
> > x(l165-1+i) = 1.60d0 + 1.4d0
> > x(l170-1+i) = 0.88857d0
> > x(l175-1+i) = -0.33421d0
> > x(l180-1+i) = -0.0018683d0
> > x(l185-1+i) = 0.00049372d0
> >
> >
> >
> >
> > --
> > regards
> >
> > Bharat Lakhani
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>

```--
regards
Bharat Lakhani
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Received on Mon Aug 03 2015 - 16:00:03 PDT
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