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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Received on Tue Feb 02 2010 - 21:00:03 PST
