I used antechamber and parmchk to add missing parameters for Pt,
steepest desent and conjugate gradiant algorithm for minimization.
&cntrl
imin = 1,
maxcyc = 10000,
ncyc = 2000,
ntb = 1,
ntr = 0,
cut = 12.0
/
Z. Khatti, Ph.D student of Physical Chemistry,
Department of Chemistry, Iran University of Science & Technology,Tehran, Iran
________________________________
From: Dr. Vitaly Chaban <vvchaban.gmail.com>
To: AMBER Mailing List <amber.ambermd.org>
Sent: Sunday, 23 February 2014, 16:56:59
Subject: Re: [AMBER] broken bond in minimization
what method did you use?
Dr. Vitaly V. Chaban
On Sun, Feb 23, 2014 at 6:35 AM, Zahra Khatti <khatti_za.yahoo.com> wrote:
> Hi amberists
>
> when I carried out a minimization for my case, two bonds including platin were broken and another bond was produced.
> my case is a platium molecule in middle of a carbon nanotube, that I added missing bond, angle and nonbond parameters for producing input.
> when I carry out a simulation by platinum molecule alone, there isn't any problem.
>
> in addition, two bonds are broken when the shake is off in minimization,
>
> since the simulation wasn't carried out when the shake was on in minimization.
> how could I resolve this problem?
>
> best regards.
>
>
>
>
> Z. Khatti, Ph.D student of Physical Chemistry,
>
> Department of Chemistry, Iran University of Science & Technology,Tehran, Iran
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Received on Sun Feb 23 2014 - 07:30:02 PST
