AMBER Archive (2005)

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

From: Ross Walker (ross_at_rosswalker.co.uk)
Date: Sun Apr 10 2005 - 13:25:16 CDT

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

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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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