Hi, I’m a PhD, who is beginning to learn about molecular modeling. I work with enzymes and for prepare it, I use the application PDB2PQR of Chimera and this software offer 6 forcefields:
- PARSE (default) - PARameters for Solvation Energy
- AMBER - AMBER ff99.
- SWANSON - AMBER ff99 charges with optimized radii.
- CHARMM - CHARMM27.
- PEOEPB - a version of Gasteiger-Marsili Partial Equalization of Orbital Electronegativities, optimized for Poisson-Boltzmann calculations.
- TYL06 - a Poisson-Boltzmann-optimized force field.
I read some about them and I think that PARSE could be a good option but I don’t know if another forcefield could be better than it. I would be very grateful if anyone could help me with this question. Thank you all for your anticipated response.
Use the default AMBER force field unless you have reasons to use another force field.
Dear Dr. Rudy J Richardson. Thank you so much for answering me. I will heed you and i will select the default force field, although it is PARSE, not AMBER. Would that be right? Thank you again for your help. Greetings
Are you using UCSF Chimera version 1.11.2? If you use this version and Tools > Structure Editing > Dock Prep and then use the defaults for each step, you will be fine. In my version, the default FF is AMBER ff14SB.
Okay, now I see that you are using the PDB2PQR tool rather than Dock Prep. Yes, for this, the default FF is PARSE. I suggest you read the documentation on this:
https://www.cgl.ucsf.edu/chimera/docs/ContributedSoftware/apbs/pdb2pqr.html
This can help you decide which tools and options to select for your purpose.
Yes, I have UCSF Chimera v 1.11.2. Oh, I will try this useful tool. Thank you so much for your kind advices. Best regards
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