AMBER Archive (2008)

Subject: Re: AMBER: running minimisation on cis-azobenzene

From: Chih-Ying Lin (chihying_at_usc.edu)
Date: Sat Apr 05 2008 - 08:33:46 CDT

Hi
Can anyone teil me any thing wrong with my revised .frcmod file ?
WIth the revised .frcmod file, cis-azobenzene still become trans-azobenzene after minimisation.

BEFORE REVISED
remark goes here
MASS

BOND

ANGLE
ca-ha-ca 0.000 0.000 ATTN, need revision
ha-ca-ha 38.000 117.650 same as ha-c2-ha

DIHE
ca-ha-ca-ca 1 0.000 0.000 0.000 ATTN, need revision
ca-ha-ca-ha 1 0.000 0.000 0.000 ATTN, need revision

IMPROPER
ca-ca-ca-ha 1.1 180.0 2.0 General improper tor
sional angle (2 general atom types)
ca-ca-ca-ne 1.1 180.0 2.0 Using default value
ca-ca-ca-nf 1.1 180.0 2.0 Using default value

NONBON

REVISED
remark goes here
MASS

BOND

ANGLE
ha-ca-ha 38.000 117.650 same as ha-c2-ha

DIHE
ca-ne-nf-ca 2 76.1904 0.000 1.0

IMPROPER
ca-ca-ca-ha 1.1 180.0 2.0 General improper tor
sional angle (2 general atom types)
ca-ca-ca-ne 1.1 180.0 2.0 Using default value
ca-ca-ca-nf 1.1 180.0 2.0 Using default value

NONBON

----- Original Message -----
From: Thomas Steinbrecher <steinbrt_at_scripps.edu>
Date: Monday, March 31, 2008 1:37 pm
Subject: Re: AMBER: running minimisation on cis-azobenzene
To: amber_at_scripps.edu

> Hi Lin,
>
> cis-transisomerization of a double bond cannot occur in a
> minimization. Is
> your starting conformation really a cis-azobenzene? Does it have
> huge
> clashes that might disrupt your structure? Unless you have very
> strange
> parameters set, what you see will indeed not occur during a
> minimization
> unless things go very wrong.
>
> Check the atom types antechamber has set for your molecule and look
> up the
> dihedrals that apply if you really have a double bond there
> (alternatingsingle-double bonds used to confuse older versions of
> antechamber, Im not
> sure that is still a danger...)
>
> Regards,
>
> Thomas
>
> Dr. Thomas Steinbrecher
> The Scripps Research Institute
> 10550 N. Torrey Pines Rd.
> San Diego CA 92037, USA
> --------------------------------------------------------------------
> ---
> The AMBER Mail Reflector
> To post, send mail to amber_at_scripps.edu
> To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu
>
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu