Re: [AMBER] Cpptraj and parmwrite and strip

From: Khabiri, Morteza <>
Date: Fri, 1 Sep 2017 19:44:20 +0000

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.



From: Khabiri, Morteza
Sent: Friday, September 1, 2017 3:37:58 PM
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.


From: Khabiri, Morteza
Sent: Friday, September 1, 2017 2:16:16 PM
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
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

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.


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Received on Fri Sep 01 2017 - 13:00:04 PDT
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