On Wed, Feb 21, 2007, Beale, John wrote:
> 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 ERROR
> ! 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?
>
Use the "desc" command in LEaP to find the real residue numbers it assigns to
each chain in your system. Then see if that helps. (Others may know more
about this particular error, but it is generally good to know that "desc" is
your friend when LEaP doesn't seem to do what you want.)
...good luck...dac
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Received on Sun Feb 25 2007 - 06:07:27 PST
