OK, this is my last posting on my LEaP problem, but this might
bite other people, so this is for the archive.
The residue definitions were initially created as prepc files,
then read into LEaP before saving as lib (off) files. The problem
turns out to be that I did not do a LEaP bondbydistance command
on the residues before saving them as lib files.
Doing this command sets a flag (17 ???) in the lib file in the
connectivity section (between O3* and C3*). Such a lib file does
not manifest the problem I have been seeing.
Bud Dodson
M. L. Dodson wrote:
>
> OK, further information on this LEaP problem. It does not have
> anything to do with the type of bond created joining the two
> halves of my covalent intermediate, as Prof. Case indicated. The
> problem was several atoms away from the region where I thought it
> was located. Skip to the bottom if you don't want the whole
> horror story.
>
> I created what I thought would be a workaround by changing the
> position where I cut the covalent intermediate into two "residues"
> so that they were no longer bonded in the LEaP script with a
> double bond (moved the cut point one carbon over). They are now
> bonded with a single C-C bond. Taking hints from the output of
> the desc command, I was able to defeat LEaP's algorithm which was
> erroneously bonding the "connect 2" atom (at the cut point) to the
> "connect 1", i.e., tail atom. LEaP also got the bonding wrong at
> the point of the (should be) -CH=NH- bond. I fixed that by
> deleting the C-N bond, then recreating it as a double bond. I
> thought this would work, but the process bombs in exactly the same
> way as before.
>
> No joy.
>
> After a lot of starts and stops, I decided to investigate the
> bogus "bond" created between the "connect 2" atom and the "connect
> 1" atom. This residue component is a ring opened deoxyribose part
> of an imine intermediate, so "connect 1" is O3*. It turns out O3*
> was not being bonded to C3*! When I forced this bond to be made,
> the topology and coordinate files were created with no problem.
>
> This seems most likely related in some way to the method I used to
> create the residues, although the mainchain topology descriptors
> were correct. I am not doing anything I know to deviate greatly
> from the canonical methods described earlier on the list.
>
> Go figure.
>
> Bud Dodson
--
M. L. Dodson
Business Email: activesitedynamics-at-comcast-dot-net
Personal Email: mldodson-at-comcast-dot-net
Phone: eight_three_two-56_three-386_one
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Received on Sun Dec 02 2007 - 06:07:10 PST
