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

[Justin Lemkul]

On 4/26/20 3:53 PM, Paolo Costa wrote:
> Dear Justin,
>
> thanks for your extra description. Very nice!
> Last doubt, which values of "phase" and "pn" should I use for [
> dihedraltypes ]?

If the force constant is zero, the remaining parameters are irrelevant.

-Justin

> Thanks again.
>
> Paolo
>
> Il giorno dom 26 apr 2020 alle ore 20:33 Justin Lemkul <jalemkul at vt.edu> ha
> scritto:
>
>>
>> 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
>>
>> ==================================================
>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
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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

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