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From: bharat lakhani <lakhbharat.gmail.com>

Date: Tue, 4 Aug 2015 11:40:42 -0400

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
*

*>
*

*>
*

*>
*

Date: Tue, 4 Aug 2015 11:40:42 -0400

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:

-- regards Bharat Lakhani _______________________________________________ AMBER mailing list AMBER.ambermd.org http://lists.ambermd.org/mailman/listinfo/amberReceived on Tue Aug 04 2015 - 09:00:02 PDT

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