pdb4amber is came from the amber-tools 15?
J.
2016-05-05 14:14 GMT+02:00 Abelak, Kavin <kabelak.rvc.ac.uk>:
> 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 - 07:00:04 PDT
