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

From: Rohanizeidanlou, Sahar <>
Date: Fri, 20 Aug 2021 00:43:41 +0000

Hi Dan,

Thanks for your reply. I just wanted to generate topology and coordinate files through CPPTRAJ. Currently cpptraj allows this process but the RADII information is getting lost. I used pqr file to generate top and crd and since pqr contains Radius information, I thought cpptraj can maintain that info throughout this process. I managed to use tleap and get the required files though.

Thanks for your help.

Best regards,
From: Daniel Roe <>
Sent: Wednesday, August 18, 2021 9:17 AM
To: AMBER Mailing List <>
Subject: Re: [AMBER] [Amber] Convert pqr to pdb

Hi, sorry for the delay in replying here, I missed it the first time around.

On Sat, Aug 14, 2021 at 5:40 PM Rohanizeidanlou, Sahar
<> wrote:
> 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?

Definitely don't use cpptraj to generate parameters! Cpptraj is really
more for manipulation of existing coordinates/topologies. In
AmberTools, you should really be using LEaP to create
topology/coordinate files.

It sounds like the issue is you want to be able to set custom GB radii
- is that the case? If so, you can use the parmed 'change RADII'
command to change the radii of atoms. I hadn't thought about cpptraj
being able to set custom radii, but maybe it's a good idea? I'll have
to think about it.

Good luck,


> Thanks,
> Sahar
> ________________________________
> From: Daniel Roe <>
> Sent: Friday, August 13, 2021 12:11 PM
> To: AMBER Mailing List <>
> 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
> <> 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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