Re: [AMBER] Split Coordinate files in Amber

From: Rohanizeidanlou, Sahar <>
Date: Fri, 16 Jul 2021 16:03:43 +0000

Hi Matthew,

Thank you so much for your help. This worked. Here's the commands I used to split complex coordinate and topology files into Guest top and crd.

#script to generate Guest top and crd from solvated complex top and crd
#load solvated complex top files
parm cb7-1.prmtop
#load solvated complex coordinates
trajin cb7-1.rst7
reference cb7-1.rst7
#trip water molecules and counterions
strip :WAT
strip :Cl-
#strip CB7 ( host )
strip :CB7 outprefix g1-dry nobox
#prepare restart output file with nobox
trajout g1-dry restart nobox
#write the output into a file
writedata g1-dry
#run the trajectory and all of the files will be saved

The same steps can be used to prepare Host top and crd files by stripping the guest molecules.

Best regards,
From: Matthew Guberman-Pfeffer <>
Sent: Tuesday, July 13, 2021 10:54 AM
To: AMBER Mailing List <>
Subject: Re: [AMBER] Split Coordinate files in Amber

Hi Sahar,

Did you try using the trajout <;;sdata=nxUfO4ctorCITOyzAgDuf69Ir7leQkkhwKqLSWODgDg%3D&amp;reserved=0> command in capptraj after using the strip <;;sdata=vTHZ2vgCr%2FnAejqou55C79y3xSH3LkC%2B95M10uEMChc%3D&amp;reserved=0> command?


> On Jul 13, 2021, at 1:49 PM, Rohanizeidanlou, Sahar <> wrote:
> *Message sent from a system outside of UConn.*
> Hello Amber Support Team,
> I have coordinate files (and topology files) of solvated complex of Protein-Ligand and I want to remove water molecule coordinates and split the remaining coordinates into Protein and Ligand coordinates. I figured how to do this for Topology files, but I couldn't find anything in Amber manual that could help with coordinate files. I appreciate if you could guide me on this.
> Thanks and best regards,
> Sahar
> _______________________________________________
> AMBER mailing list

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Received on Fri Jul 16 2021 - 09:30:02 PDT
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