Re: [AMBER] [Amber] Convert pqr to pdb from Rohanizeidanlou, Sahar on 2021-08-14 (Amber Archive Aug 2021)

From: Rohanizeidanlou, Sahar <srohani3.calstatela.edu>
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?

Thanks,
Sahar
________________________________
From: Daniel Roe <daniel.r.roe.gmail.com>
Sent: Friday, August 13, 2021 12:11 PM
To: AMBER Mailing List <amber.ambermd.org>
Subject: Re: [AMBER] [Amber] Convert pqr to pdb

Hi,

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.

-Dan

On Fri, Aug 13, 2021 at 2:21 PM Rohanizeidanlou, Sahar
<srohani3.calstatela.edu> 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
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Received on Sat Aug 14 2021 - 15:00:03 PDT