AMBER Archive (2002)

Subject: chirality.c failure - diagnosis, but no cure...

From: Michael Ford (mford_at_ccrc.uga.edu)
Date: Thu Dec 19 2002 - 12:07:07 CST

I am running xleap on a complex containing a sugar with a carboxylate
group. I am getting the following failure when I load the pdb (prep
files are loaded of course)

No C1 in aaOrig list

C1 is the carboxylate carbon, attached to one carbon and 2 oxygens.

The offending code:
        for ( i=0; i<4; i++ ) {
                for ( j=i; j<4; j++ ) {
                        if ( aaOrig[j] == aaNew[i] )
                                break;
                }
                if ( j >= 4 ) {
                        DFATAL(( "No %s in aaOrig list\n",
                                        sContainerName(aaNew[i]) ));
              
So I know that the reason I'm getting the error, is that my C1 is only
bonded to 3 atoms, and to define the chirality, this routine looks for 4
atoms. I obviously need to modify my prep file, but I'm not sure how.

A bit of the prep file:
0 0 2

Terminal 5-N-Acetyl Alpha-D-Neuraminic Acid RESP 010 6-31G*
sa.dat
SA INT 0
CORRECT OMIT DU BEG
0.0
 1 DUMM DU M 0 -1 -2 0.000 0.0 0.0 0.0
 2 DUMM DU M 1 0 -1 1.522 0.0 0.0 0.0
 3 DUMM DU M 2 1 0 1.422 109.5 0.0 0.0
 4 C2 EC M 3 2 1 1.400 113.3 180.0 0.0331
 5 C1 C B 4 3 2 1.556 111.6 -56.2 0.9623
 6 O1A O2 E 5 4 3 1.230 120.0 90.0 -0.7877
 7 O1B O2 E 5 4 3 1.230 120.0 -90.0 -0.8221

Any help is appreciated.

Mike Ford