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.
HTH,
Kavin
On 5 May 2016, at 11:39, James Starlight <jmsstarlight.gmail.com<mailto:jmsstarlight.gmail.com>> 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?
Thanks!
James
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Received on Thu May 05 2016 - 05:30:03 PDT
