Re: [AMBER] free radicals in amber

From: Ashutosh Shandilya <izerokelvin.gmail.com>
Date: Fri, 4 Feb 2011 19:39:03 +0530

 I am doing calculation for Fe -O complex where there is a free radical on
one of the oxygen. After making the library file in and adding the required
bond lengths, bond angle and dihedral parameter I was able to make the
topology and coordinate file and did the minimization. After minimization
Fe-O and the carbon attached to the free radical bond was elongated. As it
was said that amber does not understand iron or free radical. with the
attachment there is frcmod file can anyone say is there something wrong with
this frcmod file.
Although when I generated the pdb file from the topology and coordinate file
all those bonds were in the permissible limit.So I cant figure out what the
problem is.
Please have a look.
regards
*Ashutosh Shandilya*




On 27 January 2011 19:24, case <case.biomaps.rutgers.edu> wrote:

> On Thu, Jan 27, 2011, Ashutosh Shandilya wrote:
>
> > I am doing calculation for Fe -O complex where there is a free radical on
> > one of the oxygen. After making the library file in and adding the
> required
> > bond lengths, bond angle and dihedral parameter I was able to make the
> > topology and coordinate file and did the minimization.
> > So the question is can I do simulation with free radicals without
> changing
> > anything in the force fields aka .gaff file.
>
> Gaff doesn't know anything about iron, so whatever you get out will be what
> you put in by hand. Molecular mechanics doesn't know about electrons, so
> does
> not know or care whether the system is a free radical or not. But that
> means
> that whatever assumptions you make in designing the force field will show
> up
> in the results: if the input is "garbage", you know what to expect for the
> output. But if you are interested in aspects of the simulation that do not
> depend critically on how you describe the Fe-O group, you might be OK.
>
> ...dac
>
>
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>


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Received on Fri Feb 04 2011 - 06:30:04 PST
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