Re: [AMBER] How to strip water from .mdcrd file?

From: Soumendranath Bhakat <>
Date: Fri, 4 Jul 2014 09:06:25 +0200


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
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 *outtraj* command will
dump any PDB corresponding to frame number you define.

Now upload the md_dry.mdcrd and in VMD to

On Fri, Jul 4, 2014 at 3:36 AM, Wujie Wang <> 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

Thanks & Regards;
Soumendranath Bhakat
AMBER mailing list
Received on Fri Jul 04 2014 - 00:30:02 PDT
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