********>Bugfix.34:
Author: Junmei Wang, (reported by Kazua Ohta)
Date: 02/17/2005

Programs: prepgen

Description: The NEWPDB.PDB file has residue numbers in the wrong column,
             and may not give correct results when OMIT_NAMES is requested.
             There was a conditional check that was written backwards.

Fix:  apply the following patch to amber8/src/antechamber.prepgen.c

------------------------------------------------------------------------------
*** prepgen.c	2004/02/02 21:46:47	1.24
--- prepgen.c	2005/02/17 15:46:47	1.25
***************
*** 712,718 ****
  			if (seq1[j] == i)
  				seq2[i] = j;
  	for (i = 0; i < atomnum; i++)
! 		fprintf(fppdb, "%4s%7d  %-4s%3s%6d%12.3f%8.3f%8.3f%10.5f\n",
  				"ATOM", i + 1, newatom[i + 3].name, minfo.resname, 1,
  				newatom[i + 3].x, newatom[i + 3].y, newatom[i + 3].z,
  				newatom[i + 3].charge);
--- 712,718 ----
  			if (seq1[j] == i)
  				seq2[i] = j;
  	for (i = 0; i < atomnum; i++)
! 		fprintf(fppdb, "%4s%7d  %-4s%-4s%5d%12.3f%8.3f%8.3f%10.6f\n",
  				"ATOM", i + 1, newatom[i + 3].name, minfo.resname, 1,
  				newatom[i + 3].x, newatom[i + 3].y, newatom[i + 3].z,
  				newatom[i + 3].charge);
***************
*** 1024,1030 ****
  		adjustid();				/*adjust headno, tailno, mainatom etc */
  	}
  
! 	if (omitnum > 0 && charge >= 9990.) {
  		pcharge = 0.0;
  		ncharge = 0.0;
  		for (i = 0; i < atomnum; i++) {
--- 1024,1030 ----
  		adjustid();				/*adjust headno, tailno, mainatom etc */
  	}
  
! 	if (omitnum > 0 && charge <= 9990.) {
  		pcharge = 0.0;
  		ncharge = 0.0;
  		for (i = 0; i < atomnum; i++) {
  
------------------------------------------------------------------------------

Workarounds: none