Dear Amber,
bugfix24 addressed some known issues with IGB and GAFF.
However i'm having problems specifically w/ IGB=4 and GAFF.
In particular the radius of the first atom in my prep file is
of GAFF type "oh" and it ends up with a radius of 0.00000000E+00
the second to last is also of GAFF type "oh" and it ends up
with a radius of 1.00928073E+00
I am concerned that the patch to amber7/src/leap/src/leap/unitio.c in
bugfix24
did not address GAFF issues in the section of unitio.c controlled by the
statement
else if ( GDefaults.iGBparm == 4 || GDefaults.iGBparm == 5){
/* radii from
Jayaram et al. */
/* dGBrad = scale
* rStar(parm94) / (2^(1/6)) */
It seems that the following "strcmp"'s should be "strcasecmp"'s as
follows so that GAFF atoms are recognized.
I made these changes and at least the radii for the two "oh" type atoms
come out the same in my topology file
and when I run sander I get an actual number for EGB instead of EGB =
nan or EGB=inf... which a least a step in the right
direction (I hope)
***** currently in amber7/src/leap/src/leap/unitio.c *******
else if(!
strcmp(sType,"H2")) dGBrad = 1.2870;
else if(!
strcmp(sType,"H3")) dGBrad = 1.1870;
else if(!
strcmp(sType,"H4")) dGBrad = 1.4090;
else if(!
strcmp(sType,"H5")) dGBrad = 1.3590;
else if(!
strcmp(sType,"HA")) dGBrad = 1.4590;
etc... etc...
if(! strcmp(sType,"O") ||
!
strcmp(sType,"O2")) dGBrad = 1.6612;
else if(!
strcmp(sType,"OW")) dGBrad = 1.7683;E
else if(!
strcmp(sType,"OH")) dGBrad = 1.7210;
else if(!
strcmp(sType,"OS")) dGBrad = 1.6837;
********* should really be made case insensitive as follows
********************
else if(!
strcasecmp(sType,"H2")) dGBrad = 1.2870;
else if(!
strcasecmp(sType,"H3")) dGBrad = 1.1870;
else if(!
strcasecmp(sType,"H4")) dGBrad = 1.4090;
else if(!
strcasecmp(sType,"H5")) dGBrad = 1.3590;
else if(!
strcasecmp(sType,"HA")) dGBrad = 1.4590;
etc... etc...
if(! strcasecmp(sType,"O")
||
!
strcasecmp(sType,"O2")) dGBrad = 1.6612;
else if(!
strcasecmp(sType,"OW")) dGBrad = 1.7683;
else if(!
strcasecmp(sType,"OH")) dGBrad = 1.7210;
else if(!
strcasecmp(sType,"OS")) dGBrad = 1.6837;
TOm
--
-----------------------------------------
Thomas C. Bishop, Ph.D.
Joint Faculty Appointments Program Professor
Center for Bioenvironmental Research
-----------------------------------------
Tulane University Office
-----------------------------------------
Dept. of Environmental Health Sciences(SL-29)
School of Public Health & Trop. Medicine
1430 Tulane Avenue
New Orleans, LA 70112
Phone: 504-988-6203 Fax: 504-585-6428
bishop_at_tulane.edu
-----------------------------------------
Xavier University Office
-----------------------------------------
Division of Basic Pharmaceutical Sciences
College of Pharmacy
7325 Palmetto Street
New Orleans, LA 70125
Phone: 504-485-5106 Fax: 504-485-7954
tbishop_at_xula.edu
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Received on Wed Oct 16 2002 - 11:12:37 PDT
