AMBER Archive (2006)

Subject: Re: AMBER: Hybridization in leap

From: David A. Case (
Date: Tue Jul 25 2006 - 15:37:30 CDT

On Tue, Jul 25, 2006, wrote:
> I am working in Amber7 on a ligand that requires me to form more than 4
> bonds on atoms that do not normally have this many bonds. Leap crashes
> when I try to read in a pdb file with the corresponding library file
> already loaded (FATAL ERROR in chirality.c, line 115). I have found that
> bugfix.2 for Amber7 is supposed to fix this. When I try to apply the
> patch, following the directions on the amber site I get the message shown
> below.

Looks like bugfix.2 got a extra line-feed (probably from an e-mail program):
it should look like this:

*** amber.c 2001/08/02 15:02:38 7.14
--- amber.c 2002/03/08 00:23:49
*** 1446,1452 ****
                        tTypeInfo.iHybridization = HSP3;
                else {
                        VP0(( "atom type %s - unknown hybridization %s\n",
! sOString( oEntry2 ) ));
        } else if ( iObjectType(oEntry2) == OINTEGERid ) {
--- 1446,1452 ----
                        tTypeInfo.iHybridization = HSP3;
                else {
                        VP0(( "atom type %s - unknown hybridization %s\n",
! tTypeInfo.sType, sOString( oEntry2 ) ));
        } else if ( iObjectType(oEntry2) == OINTEGERid ) {

Note that the second line starting with "!" should be a complete C statment,
ending in a semicolon. (Depending on how this gets to you, that line may have
been split into two, and needs to be rejoined.)

However, it's unlikely that this is the source of your problem: bugfix.15 for
Amber 8 is more likely to help. You could try to make the changes there
"by hand" to your amber7 sources. This usually doesn't fix the problem,
but makes it easier to find out what is going on (and the error is usually in
the input pdb file, but not always).

....good luck...dac

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