[gmx-users] D-amino acids' force fields

[Mijiddorj Batsaikhan]

Hi Tsjerk,

Thank you for your reply. How can I invert the improper dihedral at the CA?
I found the D_aminoacids parameters of gromacs which supported by
SwissParam. I compaired

*ILE’s improper  of Charmm22.ff *



[ impropers ]

N             C             CA         HN

              C             CA          +N         O

[ cmap ]

-C            N             CA          C             +N



*DIL’s improper  of SwissParam modified Charmm22.ff *

[ impropers ]

                N             -C            CA          HN

                C             CA          +N          O

 [ cmap ]

                -C            N             CA          C             +N



How are the swissparam parameters reliable?


Best regards,


Mijiddorj

------------------------------

Message: 5
Date: Sat, 22 Oct 2016 10:11:50 +0200
From: Tsjerk Wassenaar <tsjerkw at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Subject: Re: [gmx-users] D-amino acids' force fields
Message-ID:
        <CABzE1Sh3MgjP8puni4mF9sk720JjaAyxaZZGg0W55vHiDaS4sA at mail.gmail.com>
Content-Type: text/plain; charset=UTF-8

Hi Mijidorj,

These amino acids are chemically and topologically equivalent to their L
counterparts. For united atom force fields you only need to invert the
improper dihedral at the C-alpha. For atomistic force fields you don't need
to change anything, except the CMAP stuff in Charmm for the backbone
dihedral, and you need to reset the hydrogen position if you used pdb2gmx
for building the topology and the hydrogens.

Cheers,

Tsjerk

On Oct 22, 2016 8:03 AM, "Mijiddorj Batsaikhan" <b.mijiddorj at gmail.com>
wrote:

> Dear users,
>
> Hello, Is there any force field that contains parameters of D-amino acids?
> In my case I need to D-ILE and D-Phe amino acids simulation. Please,
advice
> me.
>
> Best regards,
>
> Mijiddorj
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