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
> > > _______________________________________________
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> >
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> >
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Received on Tue May 10 2016 - 12:30:04 PDT
