Hello Friends, I have created an itp file for a drug by using PRODRUG. After that I have changed the charge values of the file (Using DFT). Now it is necessary to change the charge groups too? From the tutorial I observed that each charge groups are in neutral (I may be wrong). But If I use the Mullikan charges in the old file. Each charge groups have some charged value and also through Mullikan charge analysis I didn't get the same charge values for the equivalent charge groups. What should I do for this?
Taking charges directly from QM is generally not appropriate for Gromos force fields. The QM is generally just a guide to determine the electron density of various functional groups, but the force field is highly empirical and is based on condensed-phase properties, not QM target data.
Charge groups do not need to be neutral. Generally, they carry an integer charge. Using PME negates this requirement, though generally Gromos parametrization is still done with the principle of integral charges in charge groups. If using the Verlet cutoff scheme in Gromacs, charge groups are neglected entirely and the point is moot.
For most molecules, you can piece together a reasonable topology from existing building blocks and instead parametrize only the functional groups you need that are not present in the force field already. If you have any functional groups that overlap with the existing force field, you should use those parameters, not anything from QM. Force fields are highly tuned to be internally consistent; you must do all your parametrization in light of that principle.
Dear Dr. Justin,
Thank you so much for the valuable suggestion. I will make the proper itp file from the existing building blocks as you suggested.
With regards,
R. Radhika
In worst case scenario when you have no clue to group the charges, you can consider each atom as charge group, or even cancel the group-wise calculation in gromacs by using direct evaluation. This is indeed much slower but with less error than carelessly grouping the atom or adjusting charges to make charge groups integer.
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