Perhaps try using sleap. sleap adds disulfide bonds automagically
(according to some cut-off that you can set, but if the disulfide
exists in the PDB, the default is usually good enough.
Good luck!
Jason
On Tue, Feb 2, 2010 at 11:32 PM, case <case.biomaps.rutgers.edu> wrote:
> On Tue, Feb 02, 2010, Siddharth Rastogi wrote:
>
>> But when I tried with the Chain B residues, the tleap complains like
>> follows:
>>
>> > bond NF.3.SG NF.51.SG
>> bond: Argument #1 is type String must be of type: [atom]
>> usage: bond <atom1> <atom2> [order]
>
> Amber's internal residue numbers don't start over with the second chain
> (otherwise how would LEaP know that this wasn't between residues 3 and 51 in
> Chain A?).
>
> I *think* that LEaP adds 10000 to the residue numbers, so you will need
> something like "bond NF.10003.SG NF.100051.SG". But use the desc command
> to be sure -- it's been a while since I had to do this.
>
> ....dac
>
>
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--
---------------------------------------
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Wed Feb 03 2010 - 00:00:02 PST
