Re: AMBER: [SOLVED] Problem with LEaP generating topology and coord files after double bond creation

From: M. L. Dodson <>
Date: Tue, 27 Nov 2007 15:45:44 -0600

M. L. Dodson wrote:
> On Wed, Nov 21, 2007 at 05:08:08PM -0800, David A. Case wrote:
>> On Wed, Nov 21, 2007, M. L. Dodson wrote:
>>> I am including the LEaP script and the key part of the log file.
>>> I think it hangs generating the topology because the bond created
>>> is a double bond.
>> The only use Amber would make of whether this is a double bond or not is
>> in visualizing it in edit mode. That information gets lost by the
time the
>> prmtop file is made.
>> So, you should certainly see if not specifying this as a double bond
>> change anything.
> Already tried that. Changing the "D" to an "S" made no difference,
it still
> hung in the same place with the same behavior.
>> Eventually, we need to get the files you used, so that we can try to
>> the problem here.
> I'll send them on Friday when I get to the office. Should I send
> them directly to you? All of them together will be quite a bit to
> send to everyone on the list.
>>> Not Marking per-residue atom chain types.
>>> Marking per-residue atom chain types.
>>> <program hangs here, using 100% CPU>
>> This sounds evil -- somehow the tree-walking routine has probably
got lost.
>> Frustrating, because again this information is not really used for
>> I'd be very curious to know calling the cross link a double-bond is
>> the problem...we might be able to track that one down.
>> ...thanks for the report...dac
> Well, as I indicated, what I call it in the LEaP script does not
> change the behavior. I think it may have to do with the connect
> atoms that are being bonded being identified as needing a double
> bond. But I'm not familiar with the code so that may be quite off
> base.
> If there will not be a quick thing for me to change to make this
> work, please let me know. I can hack up a residue definition that
> includes both the substrate and the active site amino acid,
> burying the double bond in the middle of the residue. That way
> the residue will only have to be joined to the other molecules by
> single bonds. But that "residue" will be quite large, and I will
> need to get started working on it ASAP.
> Thanks for the response.
> Bud Dodson

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 Wed Nov 28 2007 - 06:07:41 PST
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