Dear Peter,
Thank you very much! I will use GLU0 and -nt.
Yours sincerely
Cheng
-- Original --
From: "ZHANG Cheng"<272699...@qq.com>;
Date: Tue, Jan 29, 2019 08:38 AM
To: "gromacs.org_gmx-users";
Subject: How to adjust the default protonation states in
I got an answer :)
> The GLU0 is good indeed. For the termini, it depends on the secondary
structure. Coil is the most likely for a terminus, so P5 should be OK.
Note that there is a -nt option in martinize that sets neutral termini.
> Jonathan
Peter
On 29-01-19 10:44, Peter Kroon wrote:
> Hi
Hi Zhang,
I'm fairly sure GLU0 does what you want, but I'm not 100% sure on the
terminus. It'll probably do what you want, but I've forwarded your
question to the group to be sure.
Peter
On 29-01-19 01:38, ZHANG Cheng wrote:
> Dear martini friends,
>
>
> By default, the "martinize.py" will
>
Dear martini friends,
By default, the "martinize.py" will
1) for backbone atoms, positively charge the N-terminus (atom type Qd), and
negatively charge the C-terminus (atom type Qa).
2) for side chain chargeable residues, always positively charge the LYS and ARG
and negatively charge the
