Dear AMBER users,
I have some questions concerning the Paramfit tutorial and paper.
On the tutorial, after the structures generation and validity check, we get
to the quantum calculations. From the available header, we will be
performing SP calculations.
*%RWF=job.rwf
%Chk=job.chk
%NoSave
%Mem=2GB
**#SP** b3lyp/6-31G* geom=connectivity*
On the other hand, in the paper the authors say that the:
*The CH₂–CH₂–CH₂–CH₂ alkane torsion potential was fit with Paramfit to the
energy of structures from torsion scans performed on hexane and octane
molecules evaluated using the hybrid method for interaction energies
(HM-IE).[28] Initial structures were generated from a 15° torsion scan of
hexane and octane and then optimized at the MP2/cc-pVDZ level before
performing the single-point energy calculation (Fig. 9).*
So... what's the correct way to go about this? From the paper, it looks
likes a (Gaussian?) relaxed scan every 15°, with optimization of each
conformation. But this seems contradictory to the tutorial, where, for
instance, the MM energy of every valid structure is matched to its QM
energy determined with a single point. Is someone able to clarify this?
On the other hand, both the tutorial and the paper focus on the
parametrization of dihedral angles. Does anyone have any experience
concerning the parametrization of bonds or angles? How reliable is Paramfit
for those?
Many thanks,
Best wishes,
Igor
Igor Marques, PhD Student
MSc in Pharmaceutical Biomedicine
BSc in Biomedical Sciences
Molecular Modeling Group – University of
Aveiro
http://molecular-modeling.dq.ua.pt/
Mobile phone: +351 918 567 294
Landline: +351 234 247 254
Through PBX: +351 234 370 200 (ext. 22160)
Universidade de Aveiro
Campus Universitario de Santiago
Agra do Crasto – Edificio 30
3810-193 Aveiro - Portugal
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Received on Wed Jul 27 2016 - 10:00:03 PDT
