Dear Dan,
I have downloaded and compiled ccptraj from github, now i can anchor only a
certain part of my receptor. However, in one of my system, this doesn't
solve the imaging problem. I have tried selecting different parts of my
receptor. I read in one of your response in the archive, you mentioned
about this:
center <interface 1 mask> origin
image origin center familiar com <interface 1 mask>
center <interface 2 mask> origin
image origin center familiar com <interface 2 mask> <mask excluding protein
1>
this is exactly what i want, to image the receptor first then the peptide
but still it cannot solve the problem. Is there a way that autoimage can
simultaneously image two molecules? I mean the whole complex.
Thanks!
On Mon, Jan 9, 2017 at 10:40 PM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> On Mon, Jan 9, 2017 at 3:10 AM, colvin <colvin4367.gmail.com> wrote:
> > My system consisting a receptor/protein and a peptide. The trajectories
> > post-
> > autoimage produced multiple jumps in the rmsd plot for the whole system
> > (receptor+peptide) - plot1. I can see that my peptide is jumping around
> the
> > protein (corresponds to the jump in the plot) when I viewed the
> > post-autoimage trajectory in VMD.
> >
> > However, if only the peptide or receptor rmsd is plotted, there is no
> such
> > jump as observed in the plot1. Without autoimage, the peptide wanders far
> > from the receptor at certain timestep, when viewing it with the VMD
>
> This makes sense if autoimage is not working well for your system. If
> you are calculating the RMSD of a single molecule, imaging by molecule
> has no effect. There is only an issue when you calculate the RMSD of
> multiple molecules since they may be imaged differently (which causes
> jumps).
>
> An improvement was recently made to the 'autoimage' command in the
> GitHub version of cpptraj: https://github.com/Amber-MD/cpptraj
>
> You can use the 'anchor' mask to specify only a small number of atoms
> that should remain near the center of your unit cell - this improves
> the performance of 'autoimage' in tightly packed systems.
>
> -Dan
>
> >
> > Pls advise. Thanks.
> >
> > *Plot1:*
> >
> >
> >
> >
> >
> > *rmsd_receptor:*
> >
> >
> >
> > *rmsd_peptide:*
> >
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> >
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
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>
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Received on Thu Jan 12 2017 - 21:30:03 PST
