Dalibor Trapl^1*, Martin Krupička^2*, Vladimir Višňovský^3*, Jana Hozzová^3*, Jaroslav Oľha^3*, Aleš Křenek^3*, Vojtěch Spiwok^4*

1 Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic

2 Department of Organic Chemistry, University of Chemistry and Technology, Prague, Czech Republic

3 Institute of Computer Science, Masaryk University, Brno, Czech Republic

4 Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague

* Corresponding authors emails: traplda@vscht.cz, Martin.Krupicka@vscht.cz, 467814@muni.cz, hozzova@ics.muni.cz, olha@ics.muni.cz, ljocha@ics.muni.cz, spiwokv@vscht.cz

DOI10.24435/materialscloud:yp-51 [version v1]

Publication date: Jun 01, 2021

How to cite this record

Dalibor Trapl, Martin Krupička, Vladimir Višňovský, Jana Hozzová, Jaroslav Oľha, Aleš Křenek, Vojtěch Spiwok, Property map collective variable as a useful tool for force field correction, Materials Cloud Archive 2021.84 (2021), https://doi.org/10.24435/materialscloud:yp-51

Description

Molecular mechanics potentials for small molecules suffer inaccuracies. To apply corrections we used a concept called property map to calculate corrections. It was calculated as a sum of [correction_i exp(-lambda D(x, x_i))] divided by the sum of [exp(-lambda D(x, x_i))], where correction_i is the difference between the accurate and inaccurate potential for i-th landmark structure x_i, lambda is a chosen prefactor, D is a distance (e.g. RMSD or MSD) and x are atomic coordinates. The concept was tested on alanine dipeptide (all combinations of 7 force fields, one used as a model of accurate and one as inaccurate). Next it was applied on an anticancer drug Imatinib (General AMBER Force Field corrected to DFT). Simulations were carried out in Gromacs 2016.4. Correction was Implemented using Plumed 2.4. DFT energies were calculated by ORCA 4.0 at the BP86/def2-TZVP level of theory.

Materials Cloud sections using this data

Files

File name	Size	Description
propertymapff.zip MD5md5:f88e68d79d3d677188fc277356bcae94	108.1 MiB	Input files and scripts to reproduce simulations
README MD5md5:8b512f7f16f70b5785698401d7e88a9a	7.3 KiB	README file
md5sum.txt MD5md5:8fc7bffe7dceee6317cbf3f95f0fcc8f	31.6 KiB	File fingeprtints by md5sum

License

Files and data are licensed under the terms of the following license: Creative Commons Attribution 4.0 International.
Metadata, except for email addresses, are licensed under the Creative Commons Attribution Share-Alike 4.0 International license.

External references

Keywords

molecular dynamics simulation molecular mechanics DFT free energy