Hi Hai,
thank you for your reply. could you please give a little bit more detail on
the how to properly use 'autoimage". Do you basically go to cpptraj and
type autoimage? what would be the proper steps and command to run to
autoimage? After reading some of the answers from Ambermailing list I am
scared that I might messed up the original structure or something. I looked
up the manual and I am still not clear. If you could guide be through some
steps I would really appreciate it.
Also, does that affect my analysis and calculation (like alanine scanning,
decomposition etc)? Or this is simply for the viewing purpose?
Thank you so much again,
Sincerely
RT
On Thu, May 19, 2016 at 10:26 PM, Nhai <nhai.qn.gmail.com> wrote:
> Hi
>
> You can try 'autoimage' command in cpptraj.
>
> Check the amber manual and search mail list for that. Let us know if you
> still can not solvr your issue.
>
> Cheers
> Hai
>
> > On May 19, 2016, at 10:11 PM, Arati Paudyal <apsilwal123.gmail.com>
> wrote:
> >
> > Dear all,
> >
> > Just finished a long simulation of a protein-protein complex. But when I
> > visualized the protein with VMD the entire protein changes the center
> and C
> > terminal tail of one of the proteins slowly moved out of the water box,
> > dangling out of the box. I researched and this looked like common problem
> > when iwrap=1 is used. But my question is does it matter for all the
> > analysis I just did i.e RMSD, energies,pressure .............? Do I need
> to
> > run the entire simulation without iwrap?
> >
> > On one of the questions in amber list Jason had mentioned that it is just
> > the visualization problem with vmd when iwrap is used. What do I do to
> > recenter the protein? Does simply re-centering the protein solves the
> > problem? or Do I need to rerun the simulation?
> >
> >
> > &cntrl
> > imin=0,
> > irest=1,
> > ntx=5,
> > nstlim=40000000,
> > dt=0.002,
> > ntf=2,
> > ntc=2,
> > ntxo=2,
> > ioutfm=1,
> > temp0=300.0,
> > tempi=300.0,
> > ntpr=10000,
> > ntwx=10000,
> > ntwr=10000,
> > cut=10.0,
> > iwrap=1,
> > ntb=2,
> > pres0=1.0,
> > ntp=1,
> > taup=2.0,
> > ntr=0,
> > ntt=3,
> > gamma_ln=1.0,
> > ig=-1,
> > /
> >
> > Thank you,
> >
> > RT
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>
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Received on Fri May 20 2016 - 13:00:04 PDT
