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

[Justin Lemkul]

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

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