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

[faride badalkhani]

Dear Chandan,
Thanks a lot for your answer.
Truly yours,
Farideh

On Wednesday, September 30, 2015, Chandan Choudhury <iitdckc at gmail.com>
wrote:
> 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...”*
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