********> bugfix.63
Author: Steve Gallion (Brandeis) and Bill Ross
Date:   4/23/94

Programs: LINK

Severity: Moderate

Problem: Link-modified O,H charges in DOHE residues in proteins are reversed

Affects: Proteins that use DOHE

Cause: simple programming error

	Some people like to terminate proteins with OH groups.
	A hack was introduced in LINK at some point that modified the 
	charges and default geometry of the DOHE residue (nominally 
	for DNA) ->when it was found in a protein<-, such that the net 
	charge on the OH would be neutral. However, the O received the 
	positive charge and the H the negative.

Example: This link.in, when used with db4.dat, exercises the problem:

	test


	DU
	    0    0    0    0    0
	test
	P   0    0    1    3    0
	HB  1TYR 1GLY 1ILE 1DOHE1

	QUIT


Fix:  Rather than perpetuate the hack, we provide a POHE residue (Protein 
      OH / End) having the correct charges to use instead, and the hack 
      is deleted from LINK. This will enable the same strategy to be used
      with LEaP.

Add the following residue to all.in and uni.in and rebuild db4.dat:

------------------------------------------------------------------------
PROTEIN-OH END

 POHE INT     1
 CORR OMIT DU   BEG
   0.00000
   1  DUMM  DU    M    0  -1  -2     0.000     0.000     0.000   0.00000
   2  DUMM  DU    M    1   0  -1     1.000     0.000     0.000   0.00000
   3  DUMM  DU    M    2   1   0     1.000    90.000     0.000   0.00000
   4  O     OH    M    3   2   1     1.360   113.000   180.890  -0.38000
   5  H     HO    M    4   3   2     0.960   107.000   -39.220   0.38000

DONE
------------------------------------------------------------------------

Make the following change to subroutine BLDIT in link.f (lines are
commented out with '*'s):

*** OLD link.f
--- NEW link.f
***************
*** 983,989 ****
    258 CONTINUE
        IF(MOLTYP(NMOL).NE.3) GO TO 200
        ICK = LABRES(NTOTRS)
!       IF(ICK.EQ.IDOHE) GO TO 203
  *     IF(ICK.EQ.IOME) GO TO 204
        NMINUS = NTOTRS-1
        IF(NMINUS.LE.0) GO TO 200
--- 987,993 ----
    258 CONTINUE
        IF(MOLTYP(NMOL).NE.3) GO TO 200
        ICK = LABRES(NTOTRS)
! *     IF(ICK.EQ.IDOHE) GO TO 203
  *     IF(ICK.EQ.IOME) GO TO 204
        NMINUS = NTOTRS-1
        IF(NMINUS.LE.0) GO TO 200
***************
*** 999,1010 ****
        ITYP(2,1) = IHH(4)
        ITYP(2,2) = IHH(5)
        GO TO 200
!   203 CHG(1) = 0.38
!       CHG(2) =  -0.38
!       RTP(1,1) = 1.36
!       RTP(2,1) = 113.
!       RTP(3,1) = 180.
!       RTP(2,2) = 107.
  *     GO TO 200
  * 204 CONTINUE
  *     ISYMBL(NBUILD) = IO2
--- 1003,1015 ----
        ITYP(2,1) = IHH(4)
        ITYP(2,2) = IHH(5)
        GO TO 200
! * 203 continue
! *     CHG(1) = 0.38
! *     CHG(2) =  -0.38
! *     RTP(1,1) = 1.36
! *     RTP(2,1) = 113.
! *     RTP(3,1) = 180.
! *     RTP(2,2) = 107.
  *     GO TO 200
  * 204 CONTINUE
  *     ISYMBL(NBUILD) = IO2
***************

Temporary workarounds: none.

Routines affected: BLDIT in link.f and the residue database, db4.dat.

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