Thank you so much for replying
Do you know how to strip NA+ ions also?
I add NA+ after the strip command, seems not working.
Do you know where I can find a detailed manual about cpptraj?
Thank you again.
On Fri, Jul 4, 2014 at 3:06 AM, Soumendranath Bhakat <
bhakatsoumendranath.gmail.com> wrote:
> Hii;
>
> What you can do is generate a corresponding topology and md.mdcrd file. If
> you upload the topology in VMD (in VMD choose amber parm7 during uploading
> topology) or Chimera you will get whole dynamical overview framewise. After
> loading you can go into any point of time to check.
>
> Here is a cool script you can use all in one
>
> trajin md.mdcrd
> autoimage
> strip :WAT,CL- outprefix stripped
> outtraj snaphot.pdb onlyframes 10000
> trajout md_dry.mdcrd
>
> see *outprefix* command will create a stripped topology of your original
> one something like that stripped.com_solvated.top. *outtraj* command will
> dump any PDB corresponding to frame number you define.
>
> Now upload the md_dry.mdcrd and stripped.com_solvated.top in VMD to
> visualise.
>
>
>
>
>
> On Fri, Jul 4, 2014 at 3:36 AM, Wujie Wang <wwang02.wesleyan.edu> wrote:
>
> > Dear fellow AMBER users
> >
> > I am running a water and ion-explicit DNA simulation. I want to strip all
> > the water molecules to visualize the simulation. I know cpptraj can help
> me
> > remove all the water but do not know how to do it exactly.
> >
> > I think there may be two way to do it because my purpose is just to
> > visualize the structure.
> > 1) Strip water from prmtop and mdcrd files.
> > 2) Convert mdcrd to pdb and stip water from pdb file. (This would work
> > better for my analyzing work) I already know how to convert mdcrd to pdb
> > but do not know how to strip water and ions from it.
> >
> > Can anyone tell how to do it or where I can find a document that explains
> > how to cpptraj.
> >
> > Thank you!
> >
> > Wujie
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> Thanks & Regards;
> Soumendranath Bhakat
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> AMBER mailing list
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>
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Received on Fri Jul 04 2014 - 10:00:02 PDT
