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?
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
Received on Fri Apr 04 2014 - 15:00:02 PDT
