[gmx-users] get a box of 100 molecules
Justin A. Lemkul
jalemkul at vt.edu
Fri Mar 13 15:57:38 CET 2009
Adrien Delmont wrote:
> What are the suitable options for Chirality , Full charges , Energy
> Minimization in PRODRG to get input files for hydrocarbon molecules ?
> And If I choose Full charges : YES , I will get the files that include
> charge info. Can I erase the charge info and write the charge info I
> got from Gaussian ( net charge is zero ) according to the order of atoms
> that I paste to the PRODRG screen ? Could you give me some advices about
> this ?
>
Chirality probably has to do with stereospecificity. I have never messed with
it. I figure, if I've got a stereospecific molecule, then yes, preserve
chirality. If the molecule is achiral it shouldn't matter.
If you're going to replace the charges (which is a good idea!) then the
full/reduced point is moot. I believe it has to do with the phase of the
molecule (condensed or vacuum). Simply use a text editor to adjust them in the
output topology.
EM: do you want the coordinates minimized, or not? Choose "No" if your ligand
is from a docked structure, you will want to do EM with the molecule in the
complex. If not, then you can choose "Yes" or "No" depending on what you feel
is necessary.
-Justin
> Thanks in advance
>
> Adrien
>
> ------------------------------------------------------------------------
> *From:* Justin A. Lemkul <jalemkul at vt.edu>
> *To:* adriendelmont at yahoo.com; Discussion list for GROMACS users
> <gmx-users at gromacs.org>
> *Sent:* Thursday, March 12, 2009 12:17:57 AM
> *Subject:* Re: [gmx-users] get a box of 100 molecules
>
>
>
> Adrien Delmont wrote:
> > If I create an .rtp file for my molecule how can I use this file when
> I producing gro and top files and Can I use this .rtp file with oplsaa
> and gromos 96 force fields for two different md run successfuly ?
> Because I plan to run md simulations for all atom and united atom force
> fields and compare the results. Secondly If I use PRODRG , the only
> force field I can use is oplsaa. Is it true ? Can't I use a gromos 96
> force field ?
> >
>
> I think you should start by reading the manual about .rtp files and how
> they are used. Each force field has its own .rtp, so no, you cannot use
> the same .rtp file with different force fields. Make a local copy (in
> your working directory) if you choose to modify your .rtp files; if you
> are unsure of what you are doing you can seriously screw things up.
>
> PRODRG produces Gromos-compatible force fields, not OPLS; this is
> answered in the FAQ at the PRODRG site.
>
> I reiterate: read the manual, be comfortable with how the file types are
> used, then proceed.
>
> -Justin
>
> > --- On *Wed, 3/11/09, Justin A. Lemkul /<jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>>/* wrote:
> >
> > From: Justin A. Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
> > Subject: Re: [gmx-users] get a box of 100 molecules
> > To: "Gromacs Users' List" <gmx-users at gromacs.org
> <mailto:gmx-users at gromacs.org>>
> > Date: Wednesday, March 11, 2009, 9:53 PM
> >
> > Adrien Delmont wrote:
> > > The molecule I use is a simple hydrocarbon ( n-heptane ) and I
> think that
> > I should add something like dihedral, bond, angle parameters
> after I search the
> > literature. I found some information about that. I think I will
> add parameters
> > into the related force fields .itp file. Is it true ? And then I
> will create a
> > box of 100 molecules without any error.
> > >
> > Most (if not all) of the parameters you will need will already be
> present in
> > the force field. No modification of any of these files should be
> necessary.. If
> > you want to use pdb2gmx to create your topology, you need to
> create an .rtp
> > entry. For a simple alkane (especially with a UA representation),
> it should be
> > trivial to write the topology by hand with a text editor and a
> thorough
> > understanding of Chapter 5.
> >
> > Alternate ideas:
> >
> > 1. Use PRODRG to generate a rough topology. Verify its contents before
> > proceeding, make any modifications you need, and validate the
> resulting
> > topology.
> > 2. Don't use Gromos96. AFAIK, none of the Gromos variants deal
> very well
> > with hydrocarbon chains. OPLS might be better, but I think there
> are some
> > limitations there, too.
> >
> > -Justin
> >
> > > --- On *Wed, 3/11/09, Justin A. Lemkul /<jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>>/* wrote:
> > > > From: Justin A. Lemkul <jalemkul at vt.edu
> <mailto:jalemkul at vt.edu>>
> > > Subject: Re: [gmx-users] get a box of 100 molecules
> > > To: adriendelmont at yahoo..com
> <mailto:adriendelmont at yahoo..com>, "Discussion list for GROMACS
> > users"
> > > <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> > > Date: Wednesday, March 11, 2009, 9:11 PM
> > > > Adrien Delmont wrote:
> > > > I just want to add missing parameters for my molecule in order
> > to get
> > > ...gro and top files for example GROMOS96 43a2 force field .
> How can I
> > add
> > > missing parameters ? I didn't find any information about this
> > procedure.
> > > I'm waiting for your help.
> > > > > You'll have to define what you mean by
> "parameters" - is
> > this
> > > some new small molecule that has not been parameterized under
> this
> > force field? Are you starting from scratch? If so, this is not
> a trivial
> > problem for a
> > > beginner. Read here:
> > > > http://wiki.gromacs.org/index.php/Parameterization
> > > > If you have adequate parameters for most of your
> molecule and are
> > missing
> > > something like a dihedral, etc. then read the primary
> literature and
> > derive it
> > > yourself. This process is also complicated, but is probably
> less work
> > than
> > > coming up with parameters for a brand new molecule.
> > > > -Justin
> > > > > Thanks in advance
> > > > > > --- On *Wed, 3/11/09, Mark Abraham
> > /<Mark.Abraham at anu.edu.au <mailto:Mark.Abraham at anu.edu.au>>/*
> > > wrote:
> > > > > From: Mark Abraham <Mark.Abraham at anu.edu.au
> <mailto:Mark.Abraham at anu.edu.au>>
> > > > Subject: Re: [gmx-users] get a box of 100 molecules
> > > > To: "Discussion list for GROMACS users"
> > > <gmx-users at gromacs.org <mailto:gmx-users at gromacs.org>>
> > > > Date: Wednesday, March 11, 2009, 4:58 PM
> > > > > Adrien Delmont wrote:
> > > > > > >
> > >
> ------------------------------------------------------------------------
> > > > > *From:* Adrien Delmont <adriendelmont at yahoo.com
> <mailto:adriendelmont at yahoo.com>>
> > > > > *To:* jalemkul at vt.edu <mailto:jalemkul at vt.edu>
> > > > > *Sent:* Wednesday, March 11, 2009 6:09:53 PM
> > > > > *Subject:* Re: [gmx-users] get a box of 100 molecules
> > > > > > I didn't get gro and top files with any
> > force field
> > > in Gromacs. I
> > > > basicly want to use oplsaa and GROMOS96 43a2 force field
> > (improved
> > > alkane
> > > > dihedrals) . I think I should add all the parameters
> but how
> > can I
> > > add my
> > > > parametes both into oplsaa and GROMOS96 43a2 force field ?
> > > > > You can't just mix force fields. See
> > > > http://wiki.gromacs.org/index.php/force_field
> > > > > Mark
> > > > _______________________________________________
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> ------------------------------------------------------------------------
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> > > > -- ========================================
> > > > Justin A. Lemkul
> > > Graduate Research Assistant
> > > ICTAS Doctoral Scholar
> > > Department of Biochemistry
> > > Virginia Tech
> > > Blacksburg, VA
> > > jalemkul[at]vt.edu <http://vt.edu> | (540) 231-9080
> > > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> > > > ========================================
> > > >
> > -- ========================================
> >
> > Justin A. Lemkul
> > Graduate Research Assistant
> > ICTAS Doctoral Scholar
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul[at]vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
> >
> > ========================================
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> >
> >
> > ------------------------------------------------------------------------
> >
> > _______________________________________________
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>
> -- ========================================
>
> Justin A. Lemkul
> Graduate Research Assistant
> ICTAS Doctoral Scholar
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
> ------------------------------------------------------------------------
>
> _______________________________________________
> gmx-users mailing list gmx-users at gromacs.org
> http://www.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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--
========================================
Justin A. Lemkul
Graduate Research Assistant
ICTAS Doctoral Scholar
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
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