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
Received on Fri Apr 04 2014 - 12:30:03 PDT
