You must have an old version of cpptraj. I suggest upgrading to at least
ambertools 17.
-Dan
On Fri, Sep 1, 2017 at 3:44 PM Khabiri, Morteza <khabiri.med.umich.edu>
wrote:
> I have got the parmtop run by using "outprefix" command (As suggested
> before!)
>
>
> strip :WAT,K+,Cl-,MMG,100,129 outprefix prmtop
>
>
> Please disregards my previous email.
>
>
> Thanks
>
> Morteza
>
> ________________________________
> From: Khabiri, Morteza
> Sent: Friday, September 1, 2017 3:37:58 PM
> To: amber.ambermd.org
> Subject: Re: Cpptraj and parmwrite and strip
>
>
> Thanks alot for suggestion.
>
>
> Cpptraj complain about the parmout. The error is as follow:
>
> [strip :WAT,K+,Cl-,MMG,100,129 parmout out run_strip2.prmtop]
> STRIP: Stripping atoms in mask [:WAT,K+,Cl-,MMG,100,129]
> Error: [strip] Not all arguments handled: [ parmout out run_strip2.prmtop ]
>
> It seems parmout is not an Cpptraj option. I have tried the "parmout out
> run_strip2.prmtop" on separate line and Cpptraj still complaining about
> this option. It seems the only option to write parmtop in Cpptraj is
> "parmwrite" which is not working.
>
> Thanks,
> Morteza
>
>
>
>
>
> ________________________________
> From: Khabiri, Morteza
> Sent: Friday, September 1, 2017 2:16:16 PM
> To: amber.ambermd.org
> Subject: Cpptraj and parmwrite and strip
>
>
> 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 - 13:30:02 PDT
