I can't install anything on the cluster, though. That's up to the sys admin to decide. If I can't run it on the cluster, there's no point running it on my desktop.
Cheers,
Stef
________________________________________
From: Hannes Loeffler [Hannes.Loeffler.stfc.ac.uk]
Sent: Friday, January 27, 2017 4:13 PM
To: amber.ambermd.org
Subject: Re: [AMBER] TI simulations blowing up with clambda = 1 with pmemd
The AmberTools can be downloaded for free and contain everything except
pmemd.
On Fri, 27 Jan 2017 16:09:16 +0000
Stefan Ivanov <stefan.ivanov.postgrad.manchester.ac.uk> wrote:
> " The common atoms need to have the same starting coordinates, right?
> How could they distort together? "
>
> P.S. Scratch that question. :)
>
> Anyway, so far so good.
>
> Many thanks Hannes.
>
> Best wishes,
>
> Stef
> ________________________________________
> From: Stefan Ivanov [stefan.ivanov.postgrad.manchester.ac.uk]
> Sent: Friday, January 27, 2017 4:00 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] TI simulations blowing up with clambda = 1 with
> pmemd
>
> Hi Hannes,
>
> Once again, thanks for the reply.
>
> The common atoms need to have the same starting coordinates, right?
> How could they distort together?
>
> Sadly, the cluster I'm using doesn't have Amber16, so I'll have to
> stick to 14.
>
> Best wishes,
>
> Stef
> ________________________________________
> From: Hannes Loeffler [Hannes.Loeffler.stfc.ac.uk]
> Sent: Friday, January 27, 2017 3:46 PM
> To: amber.ambermd.org
> Subject: Re: [AMBER] TI simulations blowing up with clambda = 1 with
> pmemd
>
> On Fri, 27 Jan 2017 14:54:38 +0000
> Stefan Ivanov <stefan.ivanov.postgrad.manchester.ac.uk> wrote:
>
> > Hi Hannes,
> >
> > The previous e-mail was too big to post on the mailing list; it
> > wouldn't let me.
>
> Ok.
>
>
> > Hmmm, the minimization seems to be doing the trick, although there
> > aren't any clashes in my starting structures. Also, at lamda = 1
> > BOTH ligands would become completely distorted although at that
> > lambda value the template isn't interacting with its environment at
> > all. Also, even if there were clashes between the modeled ligand
> > and any water molecules and/or ions, it wouldn't cause the whole
> > molecule to become completely distorted and keep twisting and
> > deforming throughout the whole run, let alone affect the template
> > ligand at lambda = 1.
>
> Large parts of your two ligands are single coordinate (or effective
> single topology if you like) and you have both appearing and
> disappearing parts (softcore). So most of your molecules are present
> at all times and single coordinates will distort together.
>
> I have only checked for 20000 steps of heating and 50000 steps of
> pressurising. I don't see anything that I would call distorted. One
> thought: what if instead of the lib files you have created you
> directly load the mol2 files instead and/or update to AmberTools16?
> BTW, I am on Amber16.
>
>
> > I've run 2000 steps of minimization on similar structures and I've
> > had similar problems so I'm not sure if this is a general solution
> > or works just in this particular case. I'm not really sure what's
> > going on here.
>
> I think all you need is a few tens of minimisation. When I set up the
> system I had several waters <= 2A near the ligands.
>
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Received on Fri Jan 27 2017 - 08:30:05 PST
