Dear Researchers,
I am doing molecular Dynamic simulation using GROMACS software. Currently i am working on the sugar modified double stranded DNA, for which i need to generate a force field. I tried CHARMM General Force Field, but i guess its applicable only for small molecule. I also tried GAFF where I tried generating Force field for the nucleotides(with modified sugar) by patching them with NMe/ACE. But the calculated charge on the patched group is not zero and overall charge of the nucleotide is not integer. My system has around 2000 atoms. Please suggest how I should proceed.
It is tricky to create these kind of modified residues for simulation. The easier way is to search the literature and see if some one has already optimized file for modified DNA residues and use them.
2nd, you are dealing with DNA and sugar residues, and I hope that those sugar residues are already have parameters, (DNA bases have support in multiple force fields), create the modification you want, and copy the partial charges from respective sugar and DNA (be careful for the FF consistency). You need to optimized the partial charges for the connecting and neighboring atoms, which is lot easier.
Finally, you can create everything from scratch, but it is not recommended, you need to optimize geometry, dihedrals, bond lengths, bond angles, and then assign the partial charges using either software such as Gaussian, OpenBabel, antechamber etc. This is an error prone for newbie. Plus, the FF may be adjusted for the partial charges of DNA bases in the ff files that can lead to undesirable results.
follow the tutorial:
https://ambermd.org/tutorials/advanced/tutorial1/section1.php
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