I tend to edit around-
else if (atomicnumber .eq. 12) then
> ! Mg radius = 0.99A: ref. 21 in J. Chem. Phys. 1997, 107,
> 5422
> ! Mg radius = 1.18A: ref. 30 in J. Chem. Phys. 1997, 107,
> 5422
> ! Mg radius = 1.45A: Aqvist 1992
> x(L165-1+i) = 1.18d0 + 1.4d0
> else
> write( 0,* ) 'bad atom type: ',atype
> call mexit( 6,1 )
> end if
>
When adding to the mdread file. So in your case, since you're adding in Br,
you'd have something like-
else if (atomicnumber .eq. 12) then
> ! Mg radius = 0.99A: ref. 21 in J. Chem. Phys. 1997, 107,
> 5422
> ! Mg radius = 1.18A: ref. 30 in J. Chem. Phys. 1997, 107,
> 5422
> ! Mg radius = 1.45A: Aqvist 1992
> x(L165-1+i) = 1.18d0 + 1.4d0
> ! Begin modified portion
> else if (atype == 'Br') then
> ! Br- ionic radius is 182 pm
> x(L165-1+i) = 1.82d0 + 1.4d0
> ! End modifications
> else
> write( 0,* ) 'bad atom type: ',atype
> call mexit( 6,1 )
> end if
>
Where I've assigned 1.82 to bromine using the default radius for it for Br-.
Also, you'll need to recompile Amber in serial for it to recognize the
changes to mdread.f90, otherwise you'll keep running into the bad atom type
error.
Best,
Kenneth
On Friday, April 3, 2015, Shreeramesh <shreeramesh.gmail.com> wrote:
> Dear Sir,
>
> Thanks for your response. I located mdread.F90 file and has been enclosed
> in attachment
>
> I have gone through archive "http://archive.ambermd.org/201111/0370.html"
>
> I found a phrase " bad atom type three time." Can you please kindly
> highlight me the place where the editing is required and also mention what
> needs to be edited.
>
>
> Thanks & regards
>
> *Ramesh M*
> Email: shreeramesh.gmail.com
> Mobile: (91) + 9646469938 (27) + (0) 844556164
>
>
> On Thu, Apr 2, 2015 at 8:25 AM, Kenneth Huang <kennethneltharion.gmail.com
> >
> wrote:
>
> > Shreeramesh,
> >
> > Are you looking in $AMBERHOME/src/sander? I'm assuming you have
> > AmberTools14- if so, try checking $AMBERHOME/AmberTools/src/sander for
> > mdread.F90.
> >
> > Best,
> >
> > Kenneth
> >
> > On Thu, Apr 2, 2015 at 11:15 AM, Shreeramesh <shreeramesh.gmail.com>
> > wrote:
> >
> > > On Thu, Apr 2, 2015 at 7:57 AM, Kenneth Huang <
> > kennethneltharion.gmail.com
> > > >
> > > wrote:
> > >
> > > > http://archive.ambermd.org/201111/0370.html
> > >
> > >
> > >
> > > Dear Sir,
> > >
> > > Thank for your feed back. I have gone through the archive and I was not
> > > able to locate mdread.f file as mentioned in archive
> > >
> > > Thanks & regards
> > >
> > > *Ramesh M*
> > > Email: shreeramesh.gmail.com
> > > Mobile: (91) + 9646469938 (27) + (0) 844556164
> > > _______________________________________________
> > > 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
> >
>
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Received on Fri Apr 03 2015 - 08:30:03 PDT
