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

[faride badalkhani]

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

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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