From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Thu Oct 16 2014 - 12:59:10 CDT
Thanks for guidance.
Would it be possible to combine the "grep <myname> *" command into psfgen?
Just to avoid to extract the needed particular topology from toppar_c36.
On Wed, Oct 15, 2014 at 4:20 PM, Josh Vermaas <vermaas2_at_illinois.edu> wrote:
> Hi Francesco,
> I believe they all are, although some of the combined toppar files used to
> cause NAMD problems in 2.9 (not sure about 2.10) with unrecognized
> commands. The parameter components themselves are all perfectly acceptable,
> so I would split the distributed toppar files up into separate components
> (top and par) and everything would work out just fine. For your specific
> question, its probably safe to switch to using CHARMM36 for the protein
> components, although it'd be best for you to convince yourself of that by
> reading the more recent papers describing the development of the CHARMM
> protein forcefield.
> -Josh Vermaas
> On 10/15/2014 04:34 AM, Francesco Pietra wrote:
> It is not clear to the general - mostly experimental - user, which CHARMM
> FFs for proteins, metalloproteins, and organic ligands are compatible with
> NAMD 2.10.
> For example, with namd2.10 I currently use toppar_all22_prot_heme.str for
> dioxygen in combination with top_all27 and par_all27 for the protein. Could
> I use a more recent version of CHARMM FF with that toppar? This is just an
> example, a general table of compatibility would be most welcome, especially
> in view of using CGenFF.
> francesco pietra
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