Bud, Jason,
thank you for your suggestions. I did run initial minimizations before
any further heating/density equilibration, although not with the
multistage minimization and heating, as mentioned by Bud. Will
experiment with it now.
Best,
Sasha
Jason Swails wrote:
> On Wed, Apr 13, 2011 at 4:33 PM, Sasha Buzko <obuzko.ucla.edu> wrote:
>
>
>> Thanks, Jason.
>> Manual addition of the box flag resolved the previous issue, but pmemd
>> complained about the lack of ATOMS_PER_MOLECULE records in the prmtop
>>
>>
>
> Ah, I didn't realize that your prmtop file didn't have ATOMS_PER_MOLECULE.
> That's certainly necessary. Wrapping/imaging is done based on that, as well
> as pressure scaling. I would suggest following Bud Dodson's advice, as I
> believe he has a bit of experience with packmol --> amber (you can check the
> archive for his contributions to that effect!). My comments/suggestions are
> borne completely out of my experience with the sander code and topology file
> formats, not any practical hands-on experience with packmol (even though
> I've suggested it as a tool in the past ;) ).
>
> All the best,
> Jason
>
> file. So I just reran tleap with setbox command, and everything was
>
>> taken care of. Only needed to manually correct the solvent start index
>> to make sure that both octanol and water are treated as solvent.
>>
>> Thanks again for your help
>>
>> Sasha
>>
>>
>
>
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Received on Wed Apr 13 2011 - 17:30:02 PDT
