These are just rotations around bonds, so no different parameters are
needed. It should rotate in md. If you want the initial conformation to be
syn and OE1, but you don't have initial coordinates with the hydrogen
present, you could make a pdb and load it into a tool like chimera that
allows you to manually rotate around a bond.
On Wed, Feb 1, 2023, 6:24 PM He, Amy via AMBER <amber.ambermd.org> wrote:
> Dear Amber Community,
>
> I am using Amber 20 and I intend to use leaprc.protein.ff14SB as the
> source of parameters for the standard residues in my protein.
>
> I have a quick question about simulating a protonated glutamate residue
> (GLH) with a proton on OE1. By default (in lib file “amino12.lib”, residue
> GLH has a proton named HE2 on OE2 and the configuration is syn.
>
> If I want to simulate GLH with HE1, or the anti- conformational isomers,
> do I have to make the nonstandard residues myself? Or is there any existing
> lib and/or frcmod files I can use in complementary to ff14SB?
>
>
> Many Thanks,
> Amy
>
>
> --
> Amy He
> Chemistry Graduate Teaching Assistant
> Hadad Research Group
> Ohio State University
> he.1768.osu.edu<mailto:he.1768.osu.edu>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Wed Feb 01 2023 - 16:30:04 PST
