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