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

[faride badalkhani]

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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> Gromacs Users mailing list
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