[gmx-users] bond, angles and dihedrals in the topology file

[Chandan Choudhury]

Dear Farideh,

You may have a look at
https://code.google.com/p/molecular-simulation-of-soft-matter/issues/detail?id=1
for one such example.

Chandan

On Wed, Sep 30, 2015 at 8:29 PM, faride badalkhani <
farideh.khamseh at gmail.com> wrote:

> Thank you for your time and answer. You are right, Dendrimers are composed
> of three main architectural components, a central core from which multiple
> arms emanate in an outward direction to form interior layers, and the
> reactive peripheral surface groups. Could you tell me if there is a sample
> specbond file for hyperbranched polymers?
>
> Regards,
> Farideh
>
> On Wed, Sep 30, 2015 at 6:07 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
> >
> >
> > On 9/30/15 8:24 AM, faride badalkhani wrote:
> >
> >> I want to simulate a dendrimer (a hyperbranched polymer) in water. I
> have
> >> used the GROMOS 53A6 force field parameters, and I have done the
> following
> >> steps:
> >> 1- Defining new atom types that were not exist in .atp file.
> >> 2- Adding appropriate bonds, angles, dihedrals, and impropers into the
> >> ffbonded.itp file.
> >> 3- Defining nonbonded parameters in ffnonbonded.itp file according to
> >> GROMOS FF parameters.
> >> 4- Introducing residue building blocks along with [bonds], [angles],
> >> [impropers], and [dihedrals] in .rtp file.
> >>
> >> After using pdb2gmx I receive this command:
> >>
> >> You have successfully generated a topology from: g3n.pdb
> >> The CA force field and the spce water model are used.
> >>
> >> Then I define box and solvent without any problems, but there are many
> >> errors when I execute grompp command as follows:
> >> Error 892 [file topol.top, line 6147]
> >> No default G96Angle types
> >>
> >> and
> >> Error 904 [file topol.top, line 6159]
> >> No default Proper Dih. types
> >>
> >> However, when I checked these lines I understood that
> >> 1- many of these bonds, angles, and dihedrals are related to atoms that
> >> are
> >> not connected to each other, or
> >> 2- I have defined the appropriate bond, angle, or dihedral, but I do not
> >> know why pdb2gmx didn't assign them.
> >>
> >> you can see all the files via
> >> https://www.dropbox.com/s/c8csnchfdahe016/4MEHR.zip?dl=0
> >>
> >>
> > Indeed, you have many missing interactions. This means you either have
> not
> > added all of the necessary interactions that you think you have, or your
> > connectivity is wrong. It could even be both. Just looking at the first
> > three residues, you have bonds between residues 1-2 and 1-3. pdb2gmx
> won't
> > support this; your .rtp files can only specify bonds between consecutive
> > residues via the +/- mechanism. So you're probably getting some
> unexpected
> > connectivity. I don't see any bond between atoms 1 and 27 as your first
> > message claimed. You may be able to get specbond.dat to work somehow
> here,
> > as that is the only way to assign bonds between non-consecutive residues.
> >
> > -Justin
> >
> >
> > Excuse me for my poor English,
> >>
> >> Truly yours,
> >> Farideh
> >>
> >> On Wed, Sep 30, 2015 at 3:03 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
> >>
> >>
> >>>
> >>> On 9/30/15 7:21 AM, faride badalkhani wrote:
> >>>
> >>> Dear all,
> >>>>
> >>>> Could you tell me what is wrong when there are some strange bond,
> angles
> >>>> and dihedrals in the topology file after executing pdb2gmx command?
> >>>> for example atoms 1 and 27 do not have any connectivity, but pdb2gmx
> >>>> generate them as [bonds]. A similar problem occurs in case of angles
> and
> >>>> dihedrals.
> >>>>
> >>>>
> >>>> Impossible to say without knowing what you're actually doing.  Please
> >>> always provide a full description of your system, your pdb2gmx command,
> >>> and
> >>> any relevant output, snippets of files, etc.
> >>>
> >>> -Justin
> >>>
> >>> --
> >>> ==================================================
> >>>
> >>> Justin A. Lemkul, Ph.D.
> >>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >>>
> >>> Department of Pharmaceutical Sciences
> >>> School of Pharmacy
> >>> Health Sciences Facility II, Room 629
> >>> University of Maryland, Baltimore
> >>> 20 Penn St.
> >>> Baltimore, MD 21201
> >>>
> >>> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> >>> http://mackerell.umaryland.edu/~jalemkul
> >>>
> >>> ==================================================
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> >>>
> > --
> > ==================================================
> >
> > Justin A. Lemkul, Ph.D.
> > Ruth L. Kirschstein NRSA Postdoctoral Fellow
> >
> > Department of Pharmaceutical Sciences
> > School of Pharmacy
> > Health Sciences Facility II, Room 629
> > University of Maryland, Baltimore
> > 20 Penn St.
> > Baltimore, MD 21201
> >
> > jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> > http://mackerell.umaryland.edu/~jalemkul
> >
> > ==================================================
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-- 

Chandan Kumar Choudhury
National Chemical Laboratory, Pune
India

*"All work and no play makes Jack a dull boy...”*