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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Tue May 10 2016 - 12:00:05 PDT
