Hi,
Did you recompile/reconfigure in serial? I've run into a problem when
trying to run MMPBSA in parallel after editing the mdread.f90.
Best,
Kenneth
On Tue, Aug 4, 2015 at 11:40 AM, bharat lakhani <lakhbharat.gmail.com>
wrote:
> So finally I was able to figure out what changes needed to make in
> mdread2.F90 for O3 atom type as following
>
> else if (atype == 'O3') then
> x(l165-1+i) = 1.60d0 + 1.4d0
> x(l170-1+i) = 0.0d0
> x(l175-1+i) = 0.0d0
> x(l180-1+i) = 0.0d0
> x(l185-1+i) = 0.0d0
>
> I have recompiled by doing make install but Still the same problems
> persist. Please let me know
>
> On Mon, Aug 3, 2015 at 6:50 PM, bharat lakhani <lakhbharat.gmail.com>
> wrote:
>
> > 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
> >
> >
> >
>
>
> --
> regards
>
> Bharat Lakhani
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue Aug 04 2015 - 09:30:02 PDT
