Thanks for your advice.
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. Tail residue of a DEN is connected with two head residues of
DEN, which will repeat until it has 128 DEN surface residues.
You suggested that I can create my own huge residue. In this case, is
it the best to follow your last suggestion? As far as I understand,
after I build up "super" residue, I only can connect them linearly.
How can I build up huge residues for non-linear chain? Did I
misunderstand your last suggestion?
DEN DEN
/ /
DEN DEN
\ /
DEN -DEN- COR -DEN-DEN
/ \ DEN
DEN
/ /
DEN DEN
best,
Hwankyu.
On Apr 10, 2005, at 2:25 PM, Ross Walker wrote:
> Dear Hwankyu
>
>> file, xleap tried to make COR-DEN-DEN-DEN instead of making
>> DEN-COR-DEN
>> DEN/ \DEN, and then finally show errors saying that there
>> is huge distance
>> between bonded atoms, which are not supposed to be bonded.
>> Could you tell me how to fix this problem and attach DEN
>> residues to N atoms of
>> COR??
>
> If you system forms a linear chain then you can simply change the
> order of
> the residues in the pdb file and just update the residue numbers in
> the pdb.
> However, in your case as I understand it the system is not a linear
> chain.
> The only real option you have here would be to put TER cards between
> each of
> the COR and DEN residues and then manually add the bonds you want with
> the
> bon command. I understand that this system is very big so you will
> probably
> want to automate this. Look up in the manual how leap goes about
> numbering
> residues then you could write a script to create you a leaprc file
> containing all of the bond commands that you can then source from
> within
> leap.
>
> You could also take a look at the loadpdbusingseq command in leap but I
> think this is restricted to linear chains.
>
> An alternative would be to create your own "super" residue containing
> the
> DEN-COR-DEN system as you want it and then edit the pdb and rename the
> relevant residues to use this "super" residue instead. This final
> option is
> probably the best if all of your DEN-COR-DEN topologies will be the
> same and
> you want to do this often.
>
> All the best
> Ross
>
> /\
> \/
> |\oss Walker
>
> | Department of Molecular Biology TPC15 |
> | The Scripps Research Institute |
> | Tel:- +1 858 784 8889 |
> | EMail:- ross.rosswalker.co.uk |
> | http://www.rosswalker.co.uk/ | PGP Key available on request |
>
> Note: Electronic Mail is not secure, has no guarantee of delivery, may
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>
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Received on Sun Apr 10 2005 - 22:53:01 PDT
