Hi,
On Wed, 14 Jul 2004, Sivanesan Dakshanamurthy wrote:
> when I ran 'tleap' for the given protein-ligand complex, I got the following fatal error:
>
> ___________________________________________________
> ERROR: Comparing atoms C, H251, H252, H253 to atoms N24, C, H253, H251
> !FATAL ERROR----------------------------------------
> !FATAL: In file [chirality.c], line 120
> !FATAL: Message: Atom N24 is not in the first list
> !
> !ABORTING.
> _______________________________________________
>
> NOTE: N24 atom belongs to Ligand.
>
> What may be the problem.
In the past we have noticed that
the underlying cause has been faulty connection atoms
in units produced by users.
Bugfix 15, which is actually a feature enhancement since it
merely produces a more descriptive error message, has been created
and should appear on the web soon.
Apply the patch, rebuild leap, get the residue at fault from
the new error message, and then use desc in leap to investigate
the connection atoms.
Scott
<html><body><pre>
********>Bugfix 15:
Author: Scott Brozell (reported by F.-Y. Dupradeau)
Date: 07/02/2004
Programs: LEaP
Description: tleap and xleap may produce an unclear error message when
transforming chirality orientations.
The underlying cause may be faulty connection atoms
in units produced by users.
Fix: apply the following patch to amber8/src/leap/src/leap/chirality.c
------------------------------------------------------------------------------
*** chirality.c 25 Oct 2003 23:07:18 -0000 7.3
--- chirality.c 2 Jul 2004 23:32:47 -0000
***************
*** 112,124 ****
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(( "Atom %s is not in the first list\n",
! sContainerName(aaNew[i]) ));
}
/* Swap elements and flip sign */
if ( j != i ) {
--- 112,145 ----
break;
}
if ( j >= 4 ) {
! STRING sOrigDesc[4];
! STRING sNewDesc[4];
! VP0(( "ERROR: Comparing atoms\n"
! " %s, \n"
! " %s, \n"
! " %s, and \n"
! " %s \n"
! " to atoms\n"
! " %s, \n"
! " %s, \n"
! " %s, and \n"
! " %s \n"
! " This error may be due to faulty Connection atoms.\n",
! sContainerFullDescriptor( (CONTAINER) aaOrig[0], sOrigDesc[0] ),
! sContainerFullDescriptor( (CONTAINER) aaOrig[1], sOrigDesc[1] ),
! sContainerFullDescriptor( (CONTAINER) aaOrig[2], sOrigDesc[2] ),
! sContainerFullDescriptor( (CONTAINER) aaOrig[3], sOrigDesc[3] ),
! sContainerFullDescriptor( (CONTAINER) aaNew[0], sNewDesc[0] ),
! sContainerFullDescriptor( (CONTAINER) aaNew[1], sNewDesc[1] ),
! sContainerFullDescriptor( (CONTAINER) aaNew[2], sNewDesc[2] ),
! sContainerFullDescriptor( (CONTAINER) aaNew[3], sNewDesc[3] ) ));
! /*
! Describe( cContainerWithin( aaOrig[0] ) ) ;
! Describe( cContainerWithin( aaNew[i] ) ) ;
! */
! DFATAL(( "Atom named %s from %s did not match !\n",
! sContainerName( aaNew[i] ),
! sContainerName( (CONTAINER) cContainerWithin(aaNew[i]) ) ));
}
/* Swap elements and flip sign */
if ( j != i ) {
------------------------------------------------------------------------------
Temporary workarounds are unnecessary; this is an enhancement.
</pre></body></html>
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Received on Wed Jul 14 2004 - 22:53:00 PDT
