On Fri, Apr 4, 2014 at 5:55 PM, Manikanthan Bhavaraju <
manikanthanbhavaraju.gmail.com> wrote:
> Hi Jason,
>
> Thanks for replying. Yes, it is line 2125. The lines 2078 to 2085 is:
>
> else
> ! write( 0,* ) 'bad atom type: ',atype
> ! call mexit( 6,1 )
> x(l165-1+i) = 1.70 + 1.4;
> x(l170-1+i) = 0.51245;
> x(l175-1+i) = -0.15966;
> x(l180-1+i) = -0.00019781;
> x(l185-1+i) = 0.00016392;
>
> As per your suggestion I can use a similar format for the Ca+2 ion after
> line 2125
>
> else
> !write( 0,* ) 'bad atom type: ',atype
> !call mexit( 6,1 )
> x(I165-1+i) = 1.33 + 1.4;
> x(l170-1+i) = ??;
> x(l175-1+i) = ??;
> x(l180-1+i) = ??;
> x(l185-1+i) = ??;
>
> Then, what about the values for other lines? I mean x(I170-1+i),
> x(I175-1+i), and so on. How to define these values? Can you please explain
> a bit about them?
>
Those are LCPO parameters. If you look below (line 2393) it says
>
>
> Thanks,
>
> mani
>
>
>
>
>
> On Fri, Apr 4, 2014 at 3:00 PM, Bill Ross <ross.cgl.ucsf.edu> wrote:
>
> > I don't think '==' will do assignment for you. See stmt after 'if'.
> >
> > Bill
> >
> > -------- Original message --------
> > From: Jason Swails <jason.swails.gmail.com>
> > Date:04/04/2014 10:25 AM (GMT-08:00)
> > To: amber.ambermd.org
> > Subject: Re: [AMBER] Bad atom type: C0
> >
> > On Fri, 2014-04-04 at 12:04 -0400, Mani Bhavaraju wrote:
> > > Dear All,
> > >
> > > I am trying to calculate per-residue decomposition analysis using
> > mmpbsa.py
> > > script of amber12 and ff99SB. The membrane protein + ligand system
> > > consists of Ca+2 ion. Hence, I have added the following lines to
> > > $AMBERHOME/src/sander/mdread.F90 file after line number 2215
> >
> > I assume you mean line 2125.
> >
> > >
> > > else if (atype == 'C0'.or. atype == 'Ca') then
> > > ! Ca radius = 1.3264
> > > x(L165-1+i) == 1.33d0 + 1.4d0
> >
> > The other parts of the code look like this:
> >
> > if (atomicnumber .eq. 7) then
> > x(L165-1+i) = 1.55d0 + 1.4d0
> > else if (atomicnumber .eq. 6) then
> > x(L165-1+i) = 1.70d0 + 1.4d0
> > else if (atomicnumber .eq. 1) then
> > x(L165-1+i) = 1.20d0 + 1.4d0
> > else if (atomicnumber .eq. 8) then
> > x(L165-1+i) = 1.50d0 + 1.4d0
> > else if (atomicnumber .eq. 15) then
> > x(L165-1+i) = 1.80d0 + 1.4d0
> > else if (atomicnumber .eq. 16) then
> > x(L165-1+i) = 1.80d0 + 1.4d0
> > else if (atomicnumber .eq. 12) then
> >
> > You should use "atomicnumber" instead of "atype". You can also put in
> > some write statements to make sure that sander is actually traversing
> > the code path you are modifying (standard programming debugging
> > techniques).
> >
> > You can also change the entire "else" clause to insert a default set of
> > radii (like what is done for gbsa==1 in lines 2078 to 2085 in
> > mdread.F90). Since this is just used to compute surface areas for the
> > sake of computing non-polar solvation energies, that value is probably
> > of little interest (surface area decomposition is not too well-defined
> > and only general trends are of interest in decomposition, anyway).
> >
> > HTH,
> > Jason
> >
> > --
> > Jason M. Swails
> > BioMaPS,
> > Rutgers University
> > Postdoctoral Researcher
> >
> >
> > _______________________________________________
> > 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
> >
>
>
>
> --
> Manikanthan Bhavaraju
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Apr 04 2014 - 16:30:02 PDT
