AMBER Archive (2002)

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

From: Michael Ford (mford_at_ccrc.uga.edu)
Date: Thu Dec 19 2002 - 17:25:21 CST

Sorry everyone, but this was actually a LEaP issue (xleap) with joining
our crazy branched sugars together.

Michael Ford wrote:
>
> 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