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

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

* 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:bx-gb [version v2]

Publication date: Oct 05, 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 2021.157 (2021), doi: 10.24435/materialscloud:bx-gb.

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. DFTB/MM simulation was carried out in CP2K 7.1. 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
README.txt MD5md5:8a71bba9203724c94d9433dd9363c47f	7.5 KiB	README file with a list of files
md5sum.txt MD5md5:1a147b52a6125d22a86268dd85545a06	32.9 KiB	MD5 hashes of files
propertymapff.zip MD5md5:e50e7d59bad66c7130e1f1ccef134386	109.4 MiB	Zip file containing input files

License

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External references

Keywords

molecular dynamics simulation molecular mechanics DFT free energy