The 'parmwrite' command writes out the specified topology. The 'strip'
command modifies topology information only for Actions that follow it.
What you want is an 'outprefix' or 'parmout' keyword with your strip
command to write out the stripped topology:
strip :WAT,K+,Cl-,MMG,100,129 parmout out run_strip2.parm7
It looks like you need the 'nochamber' keyword though, so you can use
parmstrip to permanently modify the topology separately:
parm run.prmtop
parmstrip :WAT,K+,Cl-,MMG,100,129
parmwrite out run_strip2.parm7 nochamber
Hope this clears things up,
-Dan
On Fri, Sep 1, 2017 at 2:16 PM, Khabiri, Morteza <khabiri.med.umich.edu> wrote:
> Hi All
>
>
> I am trying to strip the solution from my system by strip command and write the amber topology file for the stripped system. I am using the following commands:
>
> parm run.prmtop
> reference run.inpcrd
> trajin mdcrd_03.nc
> strip :WAT
> strip :K+
> strip :Cl-
> strip :MMG
> strip :100,129
> parmwrite out run_strip2.parm7 nochamber
> trajout run_strip2.pdb pdb onlyframes 1,1
> trajout run_strip.nc
>
> Unfortunately the parmwrite is writing original topology file (run.prmtop) to run_strip2.parm7. In fact there is nor strip parm file as output.
>
> Any suggestion appreciated.
>
>
> Thanks
>
> Morteza
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--
-------------------------
Daniel R. Roe
Laboratory of Computational Biology
National Institutes of Health, NHLBI
5635 Fishers Ln, Rm T900
Rockville MD, 20852
https://www.lobos.nih.gov/lcb
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Received on Fri Sep 01 2017 - 12:30:02 PDT
