[gmx-users] Lennard-Jones Parameters

[cuong nguyen]

Dear,

The top file downloaded from PRODRG did not consist of [atomtypes]. Please
tell me how can I add and use this function?

Best regards,

Cuong

On 15 October 2012 16:43, Peter C. Lai <pcl at uab.edu> wrote:

> Is there no [atomtypes] section in the top file?
>
> On 2012-10-15 03:53:54PM +0800, cuong nguyen wrote:
> > Thanks for you email.
> > I already had the .gro and .top files from PRODRG. Now I want to
> reproduce
> > these files following the LJ parameters in a published paper (charge,
> sigma
> > and epsilon values). I can change the charge in the top file, yet I do
> not
> > know how to change sigma and epsilon values.
> >
> > Best regards,
> >
> > Cuong
> >
> > On 15 October 2012 13:57, Peter C. Lai <pcl at uab.edu> wrote:
> >
> > > It's hard to understand your question. What do you mean by "reference
> > > parameters"? You said you already obtained a .gro and .top from PRODRG,
> > > which
> > > uses the gromos 43a1 forcefield to derive the parameters, so if you
> need
> > > to change the LJ parameters, edit the top file it gave you.
> > >
> > > If you want to reproduce the results of a published paper, you should
> use
> > > the
> > > forcefield and parameters specified in that paper and contact the
> author(s)
> > > if more details are needed.
> > >
> > > On 2012-10-15 10:42:57AM +0800, cuong nguyen wrote:
> > > > Thank you very much for your email, Justin.
> > > > in case I want to use the reference parameters, which force-field and
> > > what
> > > > should I do to get the .gro and .top files for this molecule?
> > > >
> > > > Best regards,
> > > >
> > > > Cuong
> > > >
> > > >
> > > > On 12 October 2012 21:14, Justin Lemkul <jalemkul at vt.edu> wrote:
> > > >
> > > > >
> > > > >
> > > > > On 10/12/12 8:04 AM, cuong nguyen wrote:
> > > > >
> > > > >>   Dear Gromacs Users,
> > > > >>
> > > > >> I got the .gro and .top files of 1-octanol downloaded from PRODRG
> > > website.
> > > > >> Please let me know if I can change charge, epsilon and sigma of
> the
> > > > >> molecule as written in a paper? and How to do?
> > > > >>
> > > > >>
> > > > > Atom types from PRODRG rarely, if ever, need changing.  Charges
> can be
> > > > > taken first by chemical homology (group-based approach that makes
> > > Gromos
> > > > > force fields convenient) and then by calculating the charges
> yourself.
> > >  For
> > > > > 1-octanol, it should be very straightforward to obtain parameters,
> zero
> > > > > charges on all the C atoms except for the one in the alocohol, then
> > > > > standard alcohol charges for the C-O-H.  Whether or not those
> > > parameters
> > > > > are sufficiently accurate is up to you to decide, but that's the
> > > approach
> > > > > one would take with this particular force field.
> > > > >
> > > > > -Justin
> > > > >
> > > > > --
> > > > > ==============================**==========
> > > > >
> > > > > Justin A. Lemkul, Ph.D.
> > > > > Research Scientist
> > > > > Department of Biochemistry
> > > > > Virginia Tech
> > > > > Blacksburg, VA
> > > > > jalemkul[at]vt.edu | (540) 231-9080
> > > > > http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<
> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
> > > > >
> > > > > ==============================**==========
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> > > ==================================================================
> > > Peter C. Lai                    | University of Alabama-Birmingham
> > > Programmer/Analyst              | KAUL 752A
> > > Genetics, Div. of Research      | 705 South 20th Street
> > > pcl at uab.edu                     | Birmingham AL 35294-4461
> > > (205) 690-0808                        |
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> ==================================================================
> Peter C. Lai                    | University of Alabama-Birmingham
> Programmer/Analyst              | KAUL 752A
> Genetics, Div. of Research      | 705 South 20th Street
> pcl at uab.edu                     | Birmingham AL 35294-4461
> (205) 690-0808                        |
> ==================================================================
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