water parameters

From: Mark Abraham (Mark.Abraham_at_anu.edu.au)
Date: Mon Aug 27 2012 - 18:29:25 CDT

Hi,

Is one meant to be able to use psfgen from NAMD 2.9 to be able to
generate a .psf for a pure TIP3P water simulation? The psfgen 1.6 user
guide suggests using top_all22_prot.inp and par_all22_prot.inp, but
http://mackerell.umaryland.edu/CHARMM_ff_params.html no longer makes
these files available (and lots of NAMD links to this site are now out
of date). The contents of
http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files/toppar_c36_aug12.tgz
are "sort of" useful, but the above files are absent and neither
toppar/toppar_water_ions.str or toppar/toppar_water_ions.prm follow the
format psfgen expects. Eventually I gave up and used some old files from
another CHARMM installation I luckily had lying around. What is the
current recommended procedure for generating a .psf for pure TIP3P, please?

Mark

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