AMBER Archive (2005)

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

From: Hwankyu Lee (leehk_at_umich.edu)
Date: Mon Apr 11 2005 - 09:49:47 CDT

Dear Ross,

Thanks for your help. I would like to make sure if I understand your
suggestion, which is shown below.
> 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.

As far as I understand your suggestion, I can generate topologies of
this molecule only manually. So, I can create some big residues
(including a lot of DEN and COR) that I can make the biggest. And then,
I can make those residues in xleap and then manually add bonds between
those big residues by "bond" command in xleap, which will reduce manual
work. Is it right?

best,
Hwankyu.

On Apr 11, 2005, at 1:00 AM, Ross Walker wrote:

> 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
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 | EMail:- ross_at_rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>
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