Got it, Thank you Bill and David.
Bill Ross wrote:
>> but can i do something about this, for example open the
>> prmtop file or the inpcrd file and 'somehow' find atom 4615 and change
>> its position?
>>
>
> Technically you could do the math to figure out which numbers
> in the inpcrd to change (consider each atom has x, y, z coords).
> Or you could generate a pdb and look at it to actually understand
> what the problem is, posssibly fixing it and regenerating prmtop
> and inpcrd.
>
> What I'd be inclined to try is some 10K dynamics (with SHAKE)
> to see if that will get you over the problem. You might even
> go on to start your equilibration from there.
>
> Bill
>
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Received on Tue Mar 16 2010 - 12:00:04 PDT
