Dear all,
If you have experience before about it, how did you parameterize the ligand for CHARMM? Is it necessary to model the ligand again e.g. using Gaussian etc. while you have the coordinates on RCSB already? After obtaining some coordinates how did you parameterize it? What about accuracy of the servers like SWISSPARAM or do you use other techniques?
Thank you very much in advance.
https://cgenff.paramchem.org/
The underlying method is explained in http://dx.doi.org/10.1002/jcc.21367
The connection between the CHARMM force field and QM is very prominent. QM dipole moments, water interaction energies, and energy scans (bond stretching, angle bending, dihedral rotations) all figure prominently as target data for deriving parameters within CHARMM. It is time-consuming, but straightforward.
Have you tried the SwissParam server?
Link below:
http://www.swissparam.ch/
ParamChem still works just fine. You can upload molecules. The NSF funding has expired, that's all, so things may evolve in new directions.
ParamChem assigns a penalty score in the output parameter file; notes on interpretation are given in the FAQ: https://cgenff.paramchem.org/commonFiles/faq.php#highpenalty
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