On Sat, May 24, 2014 at 3:39 PM, Soumendranath Bhakat <
bhakatsoumendranath.gmail.com> wrote:
> Dear Amberists;
>
> Using CPPTRAJ command I was able to generate a stripped topology
> corresponding to the stripped co-ordinate (mdcrd).
>
>
> If I delete water from the com_solvated.pdb manually will it correspond to
> the the stripped topology file?
>
> I use the following input to generate a stripped topology
>
> trajin md100.mdcrd
> autoimage
> strip :WAT,Cl- outprefix stripped
> trajout md100_dry.mdcrd
>
> Any option in CPPTRAJ to generate corresponding stripped pdb without going
> back to tleap?
>
>
cpptraj can write PDB files directly. Just add the following line to your
script:
trajout snapshot.pdb onlyframes 1
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Sat May 24 2014 - 14:00:02 PDT
