AMBER Archive (2005)

Subject: Re: AMBER: restart file and crd file

From: Lishan Yao (yaolisha_at_msu.edu)
Date: Thu Oct 27 2005 - 12:03:58 CDT

I checked the restart file. And I am interested in how water goes into
the active site.

Best,
Lishan

On Thu, 2005-10-27 at 14:35, Melinda Layten wrote:
> 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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