AMBER Archive (2000)

Subject: LEaP question

From: Jose Ramon Blas (jramon_at_sgbq.bq.ub.es)
Date: Thu Apr 13 2000 - 18:38:02 CDT

Hi amberfriends!
1) I start LEaP.
2) I load the amber parameters ( the standard ones and a .prm file that
contains some new parameters)
3) I load a library containing two new residues ( which I have created from a
pdb file following exactly the path specified in the AMBER web page).
4) Then I try to load a pdb file that contains these two residues.
5)The program, here, breaks down giving me a message like this.

!FATAL ERROR----------------------------------------
!FATAL: In file [chirality.c], line 115
!FATAL: Message: No P in aaOrig list
!
!ABORTING.
Abort

When I look to the line indicated in the chirality.c file, I find what follows:

...
   109 for ( i=0; i<4; i++ ) {
   110 for ( j=i; j<4; j++ ) {
   111 if ( aaOrig[j] == aaNew[i] )
   112 break;
   113 }
   114 if ( j >= 4 ) {
   115 DFATAL(( "No %s in aaOrig list\n",
   116 sContainerName(aaNew[i]) ));
   117 }
   118 /* Swap elements and flip sign */
   119 if ( j != i ) {
   120 SWAP( aaOrig[j], aaOrig[i], aTemp );
   121 *dPNew = -(*dPNew);
   122 }
   123 }
   124 }
   125
   126
...

Does anybody know what has happened? It would be great if anyone could give me
a possible answer.
Thanks a lot,

                                Blas