Re: [AMBER] MM-PBSA atom types

From: Jason Swails <jason.swails.gmail.com> Date: Mon, 3 Aug 2015 18:37:59 -0400

--
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
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