Hi Bill,
On 13/8/2010, at 4:19 p.m., Bill Ross wrote:
>> The first is that both sleap and tleap seem to create spurious
>> bonds between the two nickel ions, which are far enough apart
>> (3.5 to 4 Å) that they shouldn't be bonded to each other. I've
>> checked the file, and there are no CONECT records indicating that
>> the two should be bonded.
>
> I think CONECT records are ignored in any case.
> You should put a TER 'card' (line) after each
> residue that is not bonded to the one following,
> so if there are no bonds to your ions you would
> have e.g.
>
> TER
> ATOM <ion>
> TER
> ATOM <ion>
> TER
Thanks for the pointer. I guess I'd thought that calling things HETATMs and giving them different residue numbers should be sufficient. I must have been mistaken.
deleteBond in tleap got me around the problem, as well.
Cheers,
Ben
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Received on Fri Aug 13 2010 - 16:00:04 PDT
