Re: [AMBER] [Amber] Convert pqr to pdb

From: Rohanizeidanlou, Sahar <>
Date: Sat, 14 Aug 2021 21:39:59 +0000

Hi Dan,

Thank you so much for your help. I used cpptraj to generate pdb file as well as topology and coordinate files. But I realized that RADII flag is missing in the final topology file. Is it possible to tell cpptraj to maintain RADII information?

From: Daniel Roe <>
Sent: Friday, August 13, 2021 12:11 PM
To: AMBER Mailing List <>
Subject: Re: [AMBER] [Amber] Convert pqr to pdb


Cpptraj should be able to read PQR files. Try 'cpptraj -p file.pqr -y
file.pqr -x output.pdb' to convert from PQR to PDB on the command
line. See the manual for full details.


On Fri, Aug 13, 2021 at 2:21 PM Rohanizeidanlou, Sahar
<> wrote:
> Dear Amber team,
> I want to convert a pqr file to pdb format and eventually generate top and crd files. I couldn't' find any utility in Amber manual that could facilitate this. I appreciate if you could guide me on this.
> Best regards,
> Sahar
> _______________________________________________
> AMBER mailing list

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Received on Sat Aug 14 2021 - 15:00:03 PDT
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