Hi Rashid,
I just saw this. Yes, CompEL as is is not available in AMBER. You can still
calculate PMFs of permeation, or use external fields as far as I know.
If you really want to do CompEL you should still be able to prepare the
system with packmol-memgen and amber FF and transform it to Gromacs with
parmed though :D (haven't tried myself though).
Cheers,
El lun, 5 jul 2021 a las 7:14, Abdul-Rashid III Sampaco (<
absampaco.up.edu.ph>) escribió:
> Hi AMBER,
>
> I just wanted to try asking here as a last resort before moving forward.
>
> Does AMBER have the functionality for the Computational Electrophysiology
> <
> https://www.sciencedirect.com/science/article/pii/S0006349511007065?via%3Dihub
> >(compEL)
> methodology developed by Kutzner et al?
>
> It seems to be available exclusively in GROMACS. It's just that it would be
> a lot more convenient if it's also available on AMBER because of the ease
> of membrane protein system preparation provided by PACKMOL.
>
> --
> Best,
>
> Rashid
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>
--
Stephan Schott Verdugo
Biochemist
Heinrich-Heine-Universitaet Duesseldorf
Institut fuer Pharm. und Med. Chemie
Universitaetsstr. 1
40225 Duesseldorf
Germany
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Received on Fri Jul 16 2021 - 05:30:02 PDT
