AMBER Archive (2005)

Subject: RE: AMBER: A question on connecting residues in xleap

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Mon Apr 11 2005 - 00:00:34 CDT

Dear Hwankyu

> I have a question about your last suggestion. My system has one COR
> residue at the center, and has DEN residues with repeated
> pattern like
> below.

The pattern hasn't come out correctly in my email so it is a little
difficult to see exactly what you want to do.

>Tail residue of a DEN is connected with two head residues of
> DEN, which will repeat until it has 128 DEN surface residues.

I think I see what you mean. As I understand it leap will only let you make
two bonds automatically between resiudes, one to the head atom and one to
the tail. In other words each residue can only have one head and one tail.
Somebody correct me if I am wrong here. Hence you probably can't do exactly
what you want automatically in leap. However, by creating a big residue that
represents a significant chunk of your molecule you will be able to minimise
the number of bonds that you have to add manually. Your best method I think
will be to create a DEN residue and save it as a library file. Do the same
with COR. Then create some big residues out of these that represent sizeable
chunks of your molecules. Then you can load the pdb file and hopefully you
won't have too many more bonds that you have to add.

I hope this helps.
All the best
Ross

/\
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|\oss Walker

| Department of Molecular Biology TPC15 |
| The Scripps Research Institute |
| Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
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