IGB =4 with GAFF and bugfix24 incomplete?

From: Tom Bishop <bishop_at_tulane.edu>
Date: Wed 16 Oct 2002 13:12:37 -0500

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
did not address GAFF issues in the section of unitio.c controlled by the

 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;


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 
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
Received on Wed Oct 16 2002 - 11:12:37 PDT
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