Tough to saw without knowing more details. This could happen with an
unequilibrated system. I've also seen similar artifacts when
performing a system rotation (e.g. via rmsd) prior to imaging -
perhaps that's what you did here?
-Dan
On Fri, Aug 31, 2018 at 4:04 PM Yang, Tianyi <TiaYang.clarku.edu> wrote:
>
> Hi,
>
> Thank you for the help. For the cellulose system, it workd well after I added the “anchor” command into the input file. But for my protein system, cpptraj will still move the bottom layer to the top, and there will be a gap in the water box. The topology(.parm) and restart(.rst) files was generated from the xleap. Attached figure shows the system after the cpptraj. What do you think the problem might be? Do you think it is problem with my cpptraj command or xleap command?
>
> Tianyi
>
>
> ________________________________
> From: Daniel Roe <daniel.r.roe.gmail.com>
> Sent: Thursday, August 30, 2018 8:59 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] How to use cpptraj to wrap protein
>
> Hi,
>
> By default, autoimage assumes the first molecule of the system should
> be the "anchor" molecule, i.e. the molecule in the center of the
> system. In this case that is not true; the first molecule is on the
> outside of the cellulose bundle. You need to pick one near the center
> of the bundle. When I look at the cellulose bundle it appears that
> molecule 50 (residues 2010 to 2050) is close to the center, so
> something like:
>
> # Using new molecule syntax
> parm prmtop
> trajin inpcrd
> autoimage anchor ^50
> trajout out.crd
>
> will work. If you're using an old version of cpptraj that does not
> support molecule syntax you can substitute ^50 with :2010-2050, but I
> recommend upgrading to the latest version.
>
> Hope this helps,
>
> -Dan
> On Wed, Aug 29, 2018 at 8:12 PM Yang, Tianyi <TiaYang.clarku.edu> wrote:
> >
> > Hello:
> >
> > I am learning how to use cpptraj of Amber 16 to wrap the protein and water into the box. I am using the cellulose system from the Amber benchmark. The topology, restart and input files were downloaded from the Amber benchmark website. After cpptraj, water molecules were wrapped back into the box but the protein was not in the center. And it seems that the bottom of the box was moved to the top.
> >
> >
> > My cpptraj input(rst.cpptraj file):
> >
> > trajin inpcrd
> >
> > autoimage
> >
> >
> > cpptraj command:
> >
> > $AMBERHOME/bin/cpptraj -p prmtop -i rst.cpptraj &>rstcpp.log -x out.crd
> >
> >
> > Is there anything wrong with my cpptraj command or input file? The picture shows the system after the cpptraj.
> >
> >
> >
> > _______________________________________________
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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
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>
>
>
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Received on Fri Aug 31 2018 - 17:00:02 PDT
