AMBER Archive (2006)

Subject: AMBER: Hybridization in leap

Date: Tue Jul 25 2006 - 13:23:12 CDT

('binary' encoding is not supported, stored as-is) Dear Amber Community,

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
Why can the patch not be applied? Somebody please point me in the right
direction (I don't know UNIX very well).

Best Regards,


/amber7/src/leap/src/leap/ patch -c amber.c bugfix.2
Hmm... Looks like a new-style context diff to me...
The text leading up to this was:
|********>Bugfix 2:
|Author: Dave Case
|Date: 3/7/02
|Programs: tleap,xleap
|Severity: minor
|Description: LEaP may crash if an unknown hybridization is present in the
| leaprc file.
|Fix: apply the following patch to amber7/src/leap/src/leap/amber.c:
|*** amber.c 2001/08/02 15:02:38 7.14
|--- amber.c 2002/03/08 00:23:49
Patching file amber.c using Plan A...
Hunk #1 failed at 1446.
1 out of 1 hunks failed--saving rejects to amber.c.rej
Hmm... Ignoring the trailing garbage.

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