And what does "na>n" mean?
My understanding is that N should be assigned as "na" when N may be assinged as both "n" and "na", like N-acetylpyrrole.
All the best.
Azuma
-----Original Message-----
From: Junmei Wang [mailto:junmwang.gmail.com]
Sent: Tuesday, May 09, 2017 12:20 AM
To: AMBER Mailing List
Subject: Re: [AMBER] Atom type assignment by Antechamber
It is right for N in N-acetylpyrrole to be assigned as "n". The atom type definition priority does not change in GAFF2 (same as that of GAFF).
All the best
Junmei
On Mon, May 8, 2017 at 1:13 AM, Matsuura, Azuma < matsuura.azuma.jp.fujitsu.com> wrote:
> Dear all,
>
> The nitrogen atom in a pyrrole molecule should be assigned as "na" by
> its definition, and acutually Antechamber does. However, that in
> N-acetylpyrrole is assigned as "n" by Antechamber.
>
> Is it correct?
>
> In the earlier version of gaff.dat, the following message is listed;
>
> "Defination priority of nitrogen: n>n3, n>n4, n>nh, n2>n, no>n,
> na>n,
> n4>nh"
>
> Is it still in effect?
>
> Thanks in advance.
>
> All the best.
> --
> Azuma Matsuura
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon May 08 2017 - 18:30:03 PDT
