Thanks anh Hai again. Finally, we have it solved!
I actually found "outprefix stripped" in some Amber tutorials. But at that
time, I did not indicate Amber coordinates with periodic box in Vim.
I try it again today and have a look at your link, then it works well now.
Have a nice day!
Trang
On Tue, May 10, 2016 at 2:24 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
> :( my bad day. do not use "parmstrip", just "strip"
>
>
> parm com-sol.prmtop
> trajin md1.mdcrd 1 500 50
> trajin md2.mdcrd 1 500 50
> ...
> autoimage
> *strip* :WAT,Na+ outprefix strip
>
> On Tue, May 10, 2016 at 3:21 PM, Hai Nguyen <nhai.qn.gmail.com> wrote:
>
> > Hi,
> >
> > sorry for my wrong info. (too bad to use phone to reply).
> >
> > Please add "outprefix strip"
> >
> > http://archive.ambermd.org/201302/0240.html
> >
> > parm com-sol.prmtop
> > trajin md1.mdcrd 1 500 50
> > trajin md2.mdcrd 1 500 50
> > ...
> > autoimage
> > parmstrip :WAT,Na+ outprefix strip
> > ...
> >
> > after running, you will see the new stripped file: strip.com-sol.prmtop
> >
> > Hai
> >
> >
> >
> > On Tue, May 10, 2016 at 2:53 PM, Trang Nguyen <trangnt.iastate.edu>
> wrote:
> >
> >> Thanks anh Hai, but it sill not work.
> >>
> >> For some reasons, it said parmout/outparm: command not found.
> >> I already tried
> >> parm com-sol.prmtop
> >> parmstrip :WAT,Na+
> >> parmbox nobox
> >> parmwrite out new.prmtop
> >>
> >> Then, use it with md-all.mdcrd and still see distortion.
> >>
> >>
> >>
> >> On Tue, May 10, 2016 at 1:33 PM, Nhai <nhai.qn.gmail.com> wrote:
> >>
> >> > H
> >> > You used 'strip :WAT,Na+' to strip water and Na+. So you need a
> >> > corresponding prmtop file (without water and Na+).
> >> >
> >> > Try adding 'parmout new.prmtop' and use it with your stripped
> >> md-all.mdcrd
> >> >
> >> > Hai
> >> >
> >> > > On May 10, 2016, at 2:26 PM, Trang Nguyen <trangnt.iastate.edu>
> >> wrote:
> >> > >
> >> > > Hi All,
> >> > >
> >> > > I have trouble when visualizing mdcrd trajectory in VMD 1.9.2. I
> have
> >> > > searched the problem first but still cannot solve it.
> >> > >
> >> > > I would like to generate one mdcrd file (only complex of
> >> protein-ligand,
> >> > > increase time step to reduce size) from multiple mdcrd files from
> >> > > simulation. What I have tried
> >> > >
> >> > > parm com-sol.prmtop
> >> > > trajin md1.mdcrd 1 500 50
> >> > > trajin md2.mdcrd 1 500 50
> >> > > ...
> >> > > autoimage
> >> > > strip :WAT,Na+
> >> > > trajout md-all.mdcrd
> >> > > trajout md-all.pdb
> >> > >
> >> > > md-all.pdb is normally visualized with VMD. But mdcrd file cannot.
> >> (Bonds
> >> > > are distorted). I tried with com-sol.prmtop, md-all.mdcrd (Amber
> >> > coordinate
> >> > > with and without periodic box). I also make new prmtop without box
> >> > > information and WAT, but still not working.
> >> > >
> >> > > Could you please suggest me any idea to solve this problem.
> >> > >
> >> > > Thanks in advance.
> >> > > Trang
> >> > > _______________________________________________
> >> > > AMBER mailing list
> >> > > AMBER.ambermd.org
> >> > > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >> > _______________________________________________
> >> > AMBER mailing list
> >> > AMBER.ambermd.org
> >> > http://lists.ambermd.org/mailman/listinfo/amber
> >> >
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
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Received on Tue May 10 2016 - 13:00:04 PDT
