Re: [AMBER] pdb2pqr PDB processing for Amber force field

From: Abelak, Kavin <>
Date: Thu, 5 May 2016 12:14:16 +0000

Hi James,

I think what you’re looking for are “reduce” and “pdb4amber”.

Have a look at the manual for help for each of those commands. Essentially “reduce” will assign the HIE/HID/HIP to the HIS. It also has an option to flip side chains, rotate -OH groups, etc… “pdb4amber” will then take that resulting pdb and convert to an amber-friendly format.


On 5 May 2016, at 11:39, James Starlight <<>> wrote:

Hi all,

normally I use pdb2pqr utility to prepare pdb file for the submission
to tleap (e.g to assign protonation state under given PH and rename
name of the residues to the amber format).

Is it possible to do exactly the same operations (convert any pdb to
amber pdb format) using some prog from amber tools instead?



AMBER mailing list<>

[RVC Logo - link to RVC Website]<> [Twitter icon - link to RVC (Official) Twitter] <> [Facebook icon - link to RVC (Official) Facebook] <> [YouTube icon - link to RVC YouTube] <> [Pinterest icon - link to RVC Pinterest] <> [Instagram icon - link to RVC Instagram] <>

This message, together with any attachments, is intended for the stated addressee(s) only and may contain privileged or confidential information. Any views or opinions presented are solely those of the author and do not necessarily represent those of the Royal Veterinary College (RVC). If you are not the intended recipient, please notify the sender and be advised that you have received this message in error and that any use, dissemination, forwarding, printing, or copying is strictly prohibited. Unless stated expressly in this email, this email does not create, form part of, or vary any contractual or unilateral obligation. Email communication cannot be guaranteed to be secure or error free as information could be intercepted, corrupted, amended, lost, destroyed, incomplete or contain viruses. Therefore, we do not accept liability for any such matters or their consequences. Communication with us by email will be taken as acceptance of the risks inherent in doing so.
AMBER mailing list
Received on Thu May 05 2016 - 05:30:03 PDT
Custom Search