Hi,
I would like to have the vdw force field parameters of different phosphate and carbonate ionic species (eg. PO4,3- / HPO4,2- / HCO3,-) for a molecular dynamics simulation.
I'm not well familiar with charmm and amber force fields. So, my question is if I can obtain the parameters from these FFs? and if yes, which one is more sound?
I would appreciate any specific articles and/or tutorials related to my question.
Thanks in advance,
Azade
Your query is not clear to me, do you intend to use bonded interactions from CHARMM with modified non-bonded vdW interactions?
Hi. What I am trying to do is to for example solvate the ions in water. I need those parameters of the ions from charmm/amber if possible, so I guess I need both bonded and non-bonded parameters. I should not have mentioned vdw in my query, in case the bonded interactions are in other form.
you can easily generate the CHARMM parameters for these systems using:
http://www.charmm-gui.org
Hi Azade,
I hope that is useful for you.
http://research.bmh.manchester.ac.uk/bryce/amber/
Gourav Shrivastav Can you elaborate on that response?
Because whenever I try to build a phosphate buffer imitation in CHARMM-GUI using AMBER or OPLS ff (even sometimes with the CHARMM36m ff) it responds that the HPO4 force field cannot be found.
I tried using solution builder with CHARMM-GUI's own ions and with multicomponent assembler with manually built HPO4 ligands through Ligand Modeler.
Both cases refuse to work with AMBER and OPLS force fields, mostly AMBER ff.
I was building a 100A wb, with a 11 amino acid peptide, for the GROMACS suite. Standard conditions: 303.15K, Monte-Carlo placing method, no additional modifications, ligands or HET molecules from what CHARMM-GUI loads by default.
Im guessing this was the question from Azade.
- Badges
- Science topic
- Similar topics
- Engineering
- Materials Engineering
- Powders