[gmx-users] Error No default Proper Dih. types

[Justin Lemkul]

On 4/26/20 2:08 PM, Paolo Costa wrote:
> Dear Justin,
>
> thanks a  lot for your quick reply and useful information.
> Thus, I will go through to all the dihedral terms and define zero the
> corresponding force constant as you suggested. In any case, I guess it will
> be too much work to calculate also the force constant for the torsion angle
> rotation.

Metals are usually the bridge point between multiple groups and as such 
their dihedrals are all coupled and not generally considered "soft" 
(rotatable). So the conformational energetics of these molecules usually 
involves only bonds and angles in terms of internal parameters.

-Justin

> Thanks again.
>
> Paolo
>
> Il giorno dom 26 apr 2020 alle ore 20:03 Justin Lemkul <jalemkul at vt.edu> ha
> scritto:
>
>>
>> On 4/26/20 1:57 PM, Paolo Costa wrote:
>>> Dear Gromacs users,
>>>
>>> within Amber99 force field I created a new molecule, polyoxometallate, by
>>> creating a new .rtp file and modifying the atomtypes.atp, ffnonbonded.itp
>>> and the ffbondend.itp. For the ffnonbonded.itp I took the LJ parameters
>>> from known works, while the parameters for the bonding interactions I
>>> determined by Gaussian together with VFFDT software.
>>> I did not insert any parameters for the dihedral angles since the VFFTDT
>>> software does not calculated them. However as written in the related
>> paper
>>> (J. Chem. Inf. Model. 2016, 56, 811−818), *"Torsion angle rotation
>> related
>>> to metals can often be ignored".*
>>> Does somebody knows how to overcome such error in Gromacs?
>> pdb2gmx generates all possible angles and dihedrals, as determined by
>> the bonds that are defined in the .rtp entry. Thus, you likely have
>> dihedrals in the topology in which one of the participating atoms is the
>> metal. You have to have parameters for all defined interactions, but it
>> is true that dihedral terms are not typically used in this case. The
>> simplest solution is to define dihedrals with zero force constants so
>> they do not contribute to the forces in the system.
>>
>> -Justin
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Office: 301 Fralin Hall
>> Lab: 303 Engel Hall
>>
>> Virginia Tech Department of Biochemistry
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
>>
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>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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