AMBER Archive (2005)

Subject: Re: AMBER: restart file and crd file

From: Melinda Layten (mlayten_at_gmail.com)
Date: Thu Oct 27 2005 - 13:35:54 CDT

How do you know that those waters are still in the active site? You may need
to use closest waters instead.

The waters you are seeing in the active site may be stripped in your ptraj
structure since waters have a tendency to exchange.

On 27 Oct 2005 11:50:15 -0400, Lishan Yao <yaolisha_at_msu.edu> wrote:
>
> Hi Mingfeng:
>
> Then the problem may come from the ptraj part. Blow is the ptraj script
> I used for the trajectory. Water is striped except those in active site.
> Residue 1-316 is from protein. Do you know what is wrong?
>
> reference ycd.inpcrd
> trajin md_npt2.crd.gz
> rms reference out rms-ycd-cry-320k @CA
> center @CA
> image center
> strip ~:1-316,1091,5345,5702,5902,6376,8799,9524,10065,12061,12382,15338
> trajout md_npt2_waterpath.crd
> go
>
> Best,
> Lishan
>
> On Thu, 2005-10-27 at 12:11, Mingfeng Yang wrote:
> > According to my understanding, they could be, but not neccessary.
> > Because you save your snapshot into a trajectory file every ntwx steps,
> > in your case, if 500,000/ntwx = an integar, then they are the same,
> > otherwise, no.
> >
> > If I am wrong, somebody please correct me.
> >
> > Mingfeng
> >
> > Lishan Yao wrote:
> >
> > >Dear Amber users:
> > > I did a 500,000 steps MD simulation and I saved snapshots every 1000
> > >steps. My question is whether the restart file and the last snapshot in
> > >crd (trajectory) file has the same structure? The reason I ask this
> > >question is that I found out water molecules in active site have
> > >different positions in the two structures.
> > >
> > > Thank you in advance.
> > >
> > >Best,
> > >Lishan
> > >
> > >
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