Re: [AMBER] pbsa: solvation radius from topology file not used when radiopt=0

From: Ray Luo, Ph.D. <ray.luo.uci.edu>
Date: Mon, 25 Nov 2013 10:13:18 -0800

Jan-Philip,

Indeed, when you ask for potential printout, pbsa would set radii as used
in VMD for consistency. That's why it overwrites your option in the input
file. If you insist in using radiopt=0, you can certainly comment the line
"radiopt=2" output and do it again.

Ray

--
Ray Luo, Ph.D.
Professor,
Biochemistry, Molecular Biophysics, and
Biomedical Engineering
University of California, Irvine, CA 92697-3900
On Mon, Nov 25, 2013 at 10:04 AM, Jan-Philip Gehrcke <
jgehrcke.googlemail.com> wrote:
> On 11/25/2013 06:38 PM, Jan-Philip Gehrcke wrote:
>
> > I used 'set default pbradii bondi' in leap when creating that topology
> > file. I am using AmberTools 13 with the latest patches for pbsa. The
> > whole pbsa input file is this:
> >
> > &cntrl
> > inp=0,
> > /
> > &pb
> > npbopt=0,
> > radiopt=0,
> > npbverb=0,
> > space=1,
> > fillratio=1.0,
> > sasopt=2,
> > phiout=1,
> > phiform=2,
> > npbverb=1,
> > /
> >
> > So, what is the issue here? Why is the given radius not used?
> >
>
> In pb_read.F90 there is this code:
>
>     ! set phimap output options when requested
>
>     if ( phiout == 1 ) then
>        outphi = .true.
>        radiopt = 2
>        donpsa = .false.
>        npopt = 0
>     end if
>
>
> Since I am using phiout=1, radiopt becomes set to the (undocumented)
> value 2, which in turn makes pb_init() end up in this section:
>
>        else if ( radiopt == 2 ) then
>           call phi_aaradi( natom, isymbl, radi )
>
> So, if this quick analysis is right, the question would be why we set
> radiopt = 2 when phiout == 1.
>
>
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Received on Mon Nov 25 2013 - 10:30:03 PST