table of contents
| INPUTGEN(1) | User Commands | INPUTGEN(1) |
NAME¶
inputgen - manual page for inputgen 3.6.1+dfsg
DESCRIPTION¶
usage: inputgen [-h] [--asynch] [--split] [--potdx]
- [--method {para,auto,manual,async}] [--cfac CFAC] [--fadd FADD] [--space SPACE] [--gmemfac GMEMFAC] [--gmemceil GMEMCEIL] [--ofrac OFRAC] [--redfac REDFAC] [--istrng ISTRNG] filename
PDB2PQR v3.6.1: biomolecular structure conversion software. inputgen: generating APBS input files since (at least) 2004
positional arguments:¶
- filename
options:¶
- -h, --help
- show this help message and exit
- --asynch
- perform an asynchronous parallel calculation. (default: False)
- --split
- split an existing parallel input file to multiple async input files. (default: False)
- --potdx
- create an input to compute an electrostatic potential map. (default: False)
- --method {para,auto,manual,async}
- force output file to write a specific APBS ELEC method. (default: None)
- --cfac CFAC
- factor by which to expand molecular dimensions to get coarse grid dimensions. (default: 1.7)
- --fadd FADD
- amount to add to molecular dimensions to get fine grid dimensions. (default: 20.0)
- --space SPACE
- desired fine mesh resolution (default: 0.5)
- --gmemfac GMEMFAC
- number of bytes per grid point required for sequential MG calculation (default: 200)
- --gmemceil GMEMCEIL
- max MB allowed for sequential MG calculation; adjust this to force the script to perform faster calculations (which require more parallelism) (default: 400)
- --ofrac OFRAC
- overlap factor between mesh partitions (parallel) (default: 0.1)
- --redfac REDFAC
- the maximum factor by which a domain dimension can be reduced during focusing (default: 0.25)
- --istrng ISTRNG
- Ionic strength (M); Na+ and Cl- ions will be used (default: None)
| June 2023 | inputgen 3.6.1+dfsg |