Main / Medical / Toppar_water_ions.str
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18 Feb We are providing a separate version of for NAMD users. The offending lines (which are not present in said. 17 Apr Next message: Research Jubilant: "Re: FATAL ERROR: UNKNOWN PARAMETER IN CHARMM PARAMETER FILE Molecular dynamics workflow directory structure. Contribute to MD_workflow development by creating an account on GitHub.
GitHub is where people build software. More than 28 million people use GitHub to discover, fork, and contribute to over 79 million projects. Hi, all, I think the Van-der-Waals radius for calcium given in the file (parameter set 36) of the c37b2 distribution is not. toppar files : contains TIP3 water model and ion topology and parameter information. This is now the only file that contains these entities.
Second, apart from the two files you mention, you also need the stream file for water and ions (), which contains the water and ions. 31 May name @TOPPAR/ read para card flex append name @ TOPPAR/ stream 7 Oct chamber -top -param -toppar -toppar -psf. 26 Feb set e @dir/! read the protein topology read rtf card name @ a! read the protein parameters read para card flex name @b. parameters toppar/; parameters toppar/ ; # extra lipids parameters toppar/
[INPUT] topfile = # topology file parfile = # parameter file strfile = # stream file psffile = toppar_all22_prot_aliphatic_cstr. 'toppar/', 'toppar/') #prm = CharmmParameterSet('toppar/', 'toppar/' . CHARMM input file for simulation of CO in TIP3P water * set temp set nsteps stream read sequence CO3P 1 generate .