AMBER Archive (2008)

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

From: Thomas Steinbrecher (steinbrt_at_scripps.edu)
Date: Mon Apr 07 2008 - 12:39:18 CDT

What I meant is,

check if your system really has a double bond where you expect one to be
by examining the forcefield parameters and atom types set. Older versions
of antechamber/gaff sometimes did not handle complex conjugated systems
well (i.e. did not place a double bond where one should be). Since you see
cis/trans-isomerization, my guess would be that there is no double bond
set.

Regards,

Thomas

Dr. Thomas Steinbrecher
The Scripps Research Institute
10550 N. Torrey Pines Rd.
San Diego CA 92037, USA

On Mon, 7 Apr 2008, Chih-Ying Lin wrote:

>
>
> Hi Thomas:
> (alternatingsingle-double bonds used to confuse older versions of
> antechamber, Im not sure that is still a danger...)
>
> What do you mean by this ?
>
> Thanks
> Lin
>
>
>
>
>
> ----- 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
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