:( 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
>> >
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>> > AMBER.ambermd.org
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>> >
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>
>
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Received on Tue May 10 2016 - 12:30:05 PDT
