Published June 3, 2021
| Version v1.1
Dataset
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Input files for simulation of potassium channels using the AMOEBA polarizable force field
Description
This dataset contains input Tinker xyz and key files for the simulation of KcsA potassium channels in DOPC bilayer, a simple script for converting CHARMM pdb file to Tinker xyz file, and modified Tinker source code to support one-dimensional position restraints.
"params.tar.gz" contains a description of the force field modifications.
To use "mod2", add the following lines to the key file.
#compatible with amoebabio18.prm
polarize 5 1.4500 0.3900 3
polarize 11 1.4500 0.3900 9
polarize 3 1.7500 0.3900 1 5 7 50 225 227
polarize 9 1.7500 0.3900 1 7 11 50 225 227
Files
Files
(35.9 MB)
| Name | Size | Download all |
|---|---|---|
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md5:fe3e2cb2b10bff625c36c1d9857ff269
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33.1 MB | Download |
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md5:4721f20009961bd24b309d17639f42f0
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2.7 MB | Download |
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md5:d7d8a82269fe0fa4d0197db29e26bcdb
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363 Bytes | Download |
Additional details
Related works
- Is supplement to
- 10.1039/d1sc01887f (DOI)
Funding
- National Institutes of Health
- Specificity and Selectivity in Protein-Ion Binding 5R01GM114237-04
- National Institutes of Health
- DEVELOPMENT OF A NEXT-GENERATION NUCLEIC ACID FORCE FIELD 5R01GM106137-03
References
- Jing et al. Chemical Science, 2021. DOI: 10.1039/d1sc01887f