Date: Thu, 22 Oct 2015 13:37:28 -0200
Hi Pengfei,
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I am studying here your articles 2014/2015 shows where these parameters.
Use of this data for the VDW parameters created the following
files used to generate the .prmtop boot files and .inpcrd
Teste
MASS
Fe3+ 55.840
BOND
ANGLE
DIHE
IMPROPER
NONB
Fe3+ 2.886 0.0239
Teste
MASS
Zn2+ 65.370
BOND
ANGLE
DIHE
IMPROPER
NONB
Zn2+ 3.100 1.0E-6
I noticed that the model we use the following command to place the file
.prmtop
the term C4. What do I have to do? What I did so far right?
We can run the command:
parmed.py -n -O 1D23_solv.prmtop
<http://ambermd.org/tutorials/advanced/tutorial20/files/1D23_solv.prmtop>
1264_parmed.in
Step is still not done. I put a test and are minimizing with sander.
The parameters were used correctly and I now only give up command line to
incorporate the term C4?
Best regards,
Marcelo
Marcelo Andrade Chagas, MSc
(PhD student)
Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
* http://lqcmm.qui.ufmg.br/
Departamento de Química da Universidade Federal de Minas Gerais - UFMG
Tel:(31)3409-5776
2015-10-22 12:36 GMT-02:00 Pengfei Li <ambermailpengfei.gmail.com>:
> Hi Marcelo,
>
> What residues coordinate to the Fe(III) and Zn(II) ions?
>
> Best,
> Pengfei
>
> > On Oct 22, 2015, at 10:34 AM, Marcelo Andrade Chagas <
> andrade.mchagas.gmail.com> wrote:
> >
> > Dear AMBER of the list,
> >
> > How to use unbound ion model described in the tutorial:
> >
> > 12-6-4 LJ-type nonbonded model in the AMBER,
> >
> > to systems like proteins Fe(III)-M(II) ...M=Zn(II)?
> >
> > Best regards,
> >
> > Marcelo
> >
> > Marcelo Andrade Chagas, MSc
> > (PhD student)
> > Laboratório de Química Computacional e Modelagem Molecular - LQC-MM
> > * http://lqcmm.qui.ufmg.br/
> > Departamento de Química da Universidade Federal de Minas Gerais - UFMG
> > Tel:(31)3409-5776
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
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