Forwarding to amber-developers, since I know nothing about pbsa.
----- Forwarded message from Scott Brozell <sbrozell.scripps.edu> -----
Date: Thu, 9 Mar 2006 10:33:08 -0800
From: Scott Brozell <sbrozell.scripps.edu>
To: "David A. Case" <case.scripps.edu>
Subject: pbsa: nsaa bug
I may have spotted an impending bug in pbsa.
It is impending because the source file is in cvs but in the the Makefile.
In 8 there was an undocumented pb namelist variable nsaa.
In 9 there is an undocumented pb namelist variable maxarc.
It looks like nsaa has not been correctly and completely removed;
it is undeclared but:
./pb_sasa.f:447: if ( narc > nsaa*natom ) then
./pb_sasa.f:451: if ( marc(iatm) > nsaa ) then
Amber 9
Mar 09 10:30:24am loyd.scripps.edu 672> /thr/loyd/sbrozell/9/src/pbsa
f.g nsaa
./pb_sasa.f:275: allocate(knockout( nsaadot*natom), stat = alloc_err(1)
)
./pb_sasa.f:276: allocate( tmpcrd(3,nsaadot*natom), stat = alloc_err(2)
)
./pb_sasa.f:277: allocate( tmparc( nsaadot*natom), stat = alloc_err(3)
)
./pb_sasa.f:447: if ( narc > nsaa*natom ) then
./pb_sasa.f:451: if ( marc(iatm) > nsaa ) then
./pb_sasa.f:455: if ( msrf > nsaadot*natom ) then
Amber 8
Mar 09 10:22:03am loyd.scripps.edu 603> /thr/loyd/sbrozell/8/src/pbsa
f.g nsaa
./pb_force.f:96: integer :: nsaa
./pb_force.f:97: integer :: nsaadot
./pb_force.f:2853: allocate(knockout( nsaadot*natom), stat =
alloc_err(1) )
./pb_force.f:2854: allocate( sphcrd(3,nsaadot*natom), stat =
alloc_err(2) )
./pb_force.f:2855: allocate( sphcrd1(3,nsaadot*natom), stat =
alloc_err(3) )
./pb_force.f:3013: if ( narc > nsaa*natom ) then
./pb_force.f:3017: if ( marc(iatm) > nsaa ) then
./pb_force.f:3021: if ( msrf > nsaadot*natom ) then
./pb_init.f:30: radiopt, sprob, radinc, expthresh, nsas, nsaa, &
./pb_init.f:49: nsaadot= 1500
./pb_init.f:50: nsaa = 256
./pb_init.f:135: nsaadot = 1500*nint(0.5d0/arcres)
./pb_init.f:349: allocate( m2narc( nsaa ,natom), stat =
alloc_err(30) )
./pb_init.f:350: allocate( savatm(2,nsaa *natom), stat =
alloc_err(31) )
./pb_init.f:351: allocate( savctr(3,nsaa *natom), stat =
alloc_err(31) )
./pb_init.f:352: allocate( srfcrd(3,nsaadot*natom), stat =
alloc_err(33) )
----- End forwarded message -----
Received on Wed Apr 05 2006 - 23:49:41 PDT
