Dear, Hope you are doing great! I am writing this question to ask if there is an update about the parameters used for molecule parametrization. I am working with the modeling of cyclodextrin systems. My former group friend used Charmm-gui to prepare her systems, ran simulations, and published the work at Molecular Pharmaceutics. Afterward, I joined the lab and took over her studies, and tried to follow the steps she took while preparing the systems. The problem is that I am getting differences between the charges of some of the atoms of beta-cyclodextrin. Hereby, I am attaching the two files I got from Charmm-gui, namely, former.psf and current.psf : the first one was obtained by a former group friend while the other that I got from the server. I am stuck and could not understand the source of the difference. If you can help, I would really appreciate it! Thanks in advance for your help! Best,
Dear friend Mohammad Abou Chakra
It's possible that the differences you're seeing between the former and current parameter files for beta-cyclodextrin could be due to updates or improvements made to the force field or parameterization methods used by Charmm-gui since your friend's work was published. Another possibility is that there may be small differences in the input structures or simulation parameters used that could account for the differences in the resulting parameter files.
Without more specific information about the versions of Charmm-gui or the force field parameters used to generate the former and current parameter files, it's difficult to say for certain what might be causing the inconsistency you're seeing.
One thing you could try is to compare the force field parameters and charges for the specific atoms in question between the former and current parameter files and see if there are any obvious differences. You could also try contacting the Charmm-gui support team or consulting the Charmm-gui documentation to see if there have been any updates or changes to the force field parameters or parameterization methods that might account for the differences you're seeing.
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