[gmx-users] gromos96 forcefield

[Justin A. Lemkul]

Quoting Thomas Schlesier <schlesi at uni-mainz.de>:

*snip*

> The .itp file for the ohter molecule (the alkane chain is 4 atoms longer)
> looks really the same but the charges are a little bit different.
> So, have i done this right, or are there any mistakes (expect for the charge,
> see below)?
>
> One thing which i find strange are the charge of two atoms (but that this
> problem can occur was mentioned)
>      4         N     1  UNL     NAD     1    0.120  14.0067
>      5         H     1  UNL     HAH     1   -0.010   1.0080
> The N has an positive charge and the H which is bonded to the N has an
> negative charge, i expected the different. So i think i must refine the
> charges, but how?

One approach would be to assign charges based on similar functional groups found
within the force field, then follow the methodology outlined in the paper
pertaining to the derivation of the force field.  After all, it's the goal of a
force field to be as universal as possible :)  It may not be perfect, but it's a
reasonable place to start.

> Look in the paper of the force field and search there how the things were
> parameteriziesd?
>
>
> The other question that i have is, what is the difference between the .gro
> and the .g96 file?
> I thought .gro is for the gromos87 force field and .g96 is for all the
> gromos96 force fields.

The .gro extension means that it is a Gromacs coordinate file.  The .g96
extension is the format taken by the Gromos96 program.  This should not be
confused with the Gromos96 force fields.  Coordinate files are not dependent
upon the force field used, but rather the software.

For some general information, check this out:
http://www.gromacs.org/documentation/reference/online/files.html

-Justin

> But prodrg gives me for both force field an coordinate file which looks from
> the format like a .gro file.
> And on the internet i found an tutorial
> (http://md.chem.rug.nl/education/Free-Energy_Course/2.hydration-fe.html) in
> which pdb2gmx was used for an gromos96 force field but the
> coordinate file was in the end a .gro file
> -> so i am some what confused
>
> Thomas
>
>
> > Message: 1
> > Date: Fri, 9 May 2008 14:43:04 +0200
> > From: Thomas Schlesier <schlesi at uni-mainz.de>
> > Subject: [gmx-users] gromos96 forcefield
> > To: "gmx-users at gromacs.org" <gmx-users at gromacs.org>
> > Message-ID: <482446D8.3070102 at uni-mainz.de>
> > Content-Type: text/plain; charset="ISO-8859-15"
> >
> > dear all,
> > till now i simulated with the gromos87 forcefield, but now i want to
> > change it.
> > i have two small molecules which consist of a short alkane chain and
> > then an urea-group.
> >
> > i built my molecules with spartan and saved them as .pdb then i tried
> > pdb2gmx, but this failed:
> > Fatal error:
> > Residue 'UNK' not found in residue topology database
> > but i have no idea how i should name the residues so that they are found
> > in the database.
> > then i tried pdb2gmx with my .gro file (which i get from prodrg with the
> > .pdb file), but here the same problem occured.
> >
> > the other thing that i tried was to make the files with the beta version
> > of prodrg. i get the .gro/.g96 and .itp files but they look the same
> > like the files for the gromos87 forcefield (different values but the
> > same format).
> > i used editconf on the .g96 file but it doesn't really work, the new
> > .g96 file looks like:
> >
> > TITLE
> >
> > END
> > POSITION
> > END
> > BOX
> >    10.000000000   10.000000000   10.000000000
> > END
> >
> > from that and the gromacs-user manual i get the idea that .gro and .96
> > files use different formats, but i don't really know how the format for
> > .g96 looks like (i looked for a user manual for gromos96, but didn't
> > found one for free).
> >
> > so the question is:
> > 1) is there a way to translate the gromos87 files to gromos96?
> > or
> > 2) what should i do with the files form prodrg beta that they work?
> >
> > thanks for an answer
> > thomas
> >
> >
> > ------------------------------
> >
> > Message: 2
> > Date: Fri,  9 May 2008 08:54:55 -0400
> > From: "Justin A. Lemkul" <jalemkul at vt.edu>
> > Subject: Re: [gmx-users] gromos96 forcefield
> > To: Discussion list for GROMACS users <gmx-users at gromacs.org>
> > Message-ID: <1210337695.4824499f76762 at webmail.vt.edu>
> > Content-Type: text/plain; charset=ISO-8859-1
> >
> > Quoting Thomas Schlesier <schlesi at uni-mainz.de>:
> >
> >
> >> dear all,
> >> till now i simulated with the gromos87 forcefield, but now i want to
> >> change it.
> >> i have two small molecules which consist of a short alkane chain and
> >> then an urea-group.
> >>
> >> i built my molecules with spartan and saved them as .pdb then i tried
> >> pdb2gmx, but this failed:
> >> Fatal error:
> >> Residue 'UNK' not found in residue topology database
> >> but i have no idea how i should name the residues so that they are found
> >> in the database.
> >> then i tried pdb2gmx with my .gro file (which i get from prodrg with the
> >> .pdb file), but here the same problem occured.
> >>
> >
> > Right, because pdb2gmx does not magically produce parameters for any
> molecule
> > you'd like.  Check the .rtp file for the force field you're interested in;
> it
> > will show you the residues/molecules for which parameters exist.
> >
> >
> >> the other thing that i tried was to make the files with the beta version
> >> of prodrg. i get the .gro/.g96 and .itp files but they look the same
> >> like the files for the gromos87 forcefield (different values but the
> >> same format).
> >>
> >
> > They should look the same; the different parameters are what you're after.
> Be
> > aware that PRODRG produces charges/charge groups that are often
> unsatisfactory
> > and need refining.
> >
> >
> >> i used editconf on the .g96 file but it doesn't really work, the new
> >> .g96 file looks like:
> >>
> >> TITLE
> >>
> >> END
> >> POSITION
> >> END
> >> BOX
> >>    10.000000000   10.000000000   10.000000000
> >> END
> >>
> >> from that and the gromacs-user manual i get the idea that .gro and .96
> >> files use different formats, but i don't really know how the format for
> >> .g96 looks like (i looked for a user manual for gromos96, but didn't
> >> found one for free).
> >>
> >> so the question is:
> >> 1) is there a way to translate the gromos87 files to gromos96?
> >> or
> >> 2) what should i do with the files form prodrg beta that they work?
> >>
> >
> > I'm not quite sure what you're after in these, but I can tell you the
> following:
> >
> > 1. You don't translate one force field to another, in terms of some simple
> > conversion.  You derive new parameters, or use parameters from a
> > well-documented, trusted source.  In terms of .g96 --> .gro conversion,
> > editconf should have done the trick.  What was the command you tried, and
> was
> > the .g96 file properly formatted?
> >
> > 2. You use the .itp file you get from PRODRG, verify the validity of the
> > parameters, and proceed.
> >
> > -Justin
> >
> >
> >> thanks for an answer
> >> thomas
> >> _______________________________________________
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> >>
> >
> >
> >
> > ========================================
> >
> > Justin A. Lemkul
> > Graduate Research Assistant
> > Department of Biochemistry
> > Virginia Tech
> > Blacksburg, VA
> > jalemkul at vt.edu | (540) 231-9080
> > http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/
> >
> > ========================================
>



========================================

Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul at vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/

========================================