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 <jalem...@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
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Justin A. Lemkul, Ph.D.
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Office: 301 Fralin Hall
Lab: 303 Engel Hall
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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
jalem...@vt.edu | (540) 231-3129
http://www.thelemkullab.com
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