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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Received on Tue May 10 2016 - 12:00:03 PDT
