AMBER: LEaP Problem

From: Beale, John <>
Date: Wed, 21 Feb 2007 07:11:13 -0600

I am trying to build the *.top and *.crd files for a small protein. The
molecule has 7 disulfide bonds. I have been trying to use the "bond"
command in LEaP to build the disulfide linkages. If I do a
"saveAmberParm" before I do the disulfide bonding, the *.top and *.crd
files are built normally. If I bond the disulfides (using neu.10.SG
neu.54.SG, for example), LEaP crashes. This is the error message that I
get after the crash:



! FATAL: In file [unitio.c], line 1769

! FATAL: Message: 1-4: cannot add bond 104 701




A little more information about the protein: the molecule is a dimer
possessing identical amino acid sequences in both monomeric components.
The CYX residues have identical residue numbers in both chains. I
suppose that it is possible that LEaP is trying, and failing, to build a
disulfide bond between a CYX residue in chain A and one with its pair
number in chain B. If this is what is causing LEaP to crash, is there a
way to execute the "bond" step designating that the disulfide bond
should be created within the same chain?


Has anyone had this happen and found a solution?





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Received on Sun Feb 25 2007 - 06:07:04 PST
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