AMBER Archive (2003)

Subject: Re: AMBER: problem in tleap

From: Scott Brozell (sbrozell_at_scripps.edu)
Date: Fri Oct 24 2003 - 21:05:33 CDT

Hello,

Basically leap is comparing the orientation of two lists of
atoms to determine the correct torsion values (model.c,
dModelCalculateOrientation).
Probably your problem boils down to operator error; to localize the error
you could add this extra printing to chirality.c
*** 112,118 ****
            break;
      }
      if ( j >= 4 ) {
! DFATAL(( "No %s in aaOrig list\n",
               sContainerName(aaNew[i]) ));
      }
      /* Swap elements and flip sign */
--- 112,123 ----
            break;
      }
      if ( j >= 4 ) {
! VP0(( "ERROR: Comparing atoms %s, %s, %s, %s to atoms %s, %s, %s, %s\n",
! sContainerName(aaOrig[0]), sContainerName(aaOrig[1]),
! sContainerName(aaOrig[2]), sContainerName(aaOrig[3]),
! sContainerName(aaNew[0]), sContainerName(aaNew[1]),
! sContainerName(aaNew[2]), sContainerName(aaNew[3]) ));
! DFATAL(( "No atom %s in first list\n",
               sContainerName(aaNew[i]) ));
      }
      /* Swap elements and flip sign */

Alternatively or additionally you could build leap with debugging on.
I think all you have to do is change in src/leap/Imakefile
#define LeapDebugLib NO
to
#define LeapDebugLib YES

Good luck,

Scott Brozell

On Fri, 24 Oct 2003 aini_at_UMDNJ.EDU wrote:

> Thanks for dac's suggestions!
> I deleted the three atoms and then tleap stopped complaining about the end
> phosphate group. However the fatal error is still there. And I checked my pdb
> file and believe there is not extra atom. What else may give this fatal message?
>
> aini
>
> Quoting "David A. Case" <case_at_scripps.edu>:
>
> > On Fri, Oct 17, 2003, aini_at_UMDNJ.EDU wrote:
> > >
> > > !FATAL ERROR----------------------------------------
> > > !FATAL: In file [chirality.c], line 115
> > > !FATAL: Message: No C5 in aaOrig list
> > > !
> > > !ABORTING.
> > >
> > > The "DC5 329" is the 5'-Cytosine in one DNA strain. I found "chirality.c"
> > file
> > > but I don't know what the aaOrig list means.
> > >
> >
> > I'm not sure about this one, but it plausibly is related to the extra atoms
> > in
> > your pdb file. Can you remove the three atoms listed above, and see what
> > happens?
> >
> > ..dac
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