I just figured it out. It should be Cl instead of CL and Na instead of NA.
Thank you so much!
On Fri, Jul 4, 2014 at 12:48 PM, Wujie Wang <wwang02.wesleyan.edu> wrote:
> 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Fri Jul 04 2014 - 10:00:03 PDT
