From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Thu Oct 16 2014 - 13:45:05 CDT
True, grep totally cannot be relied upon for this purpose, to the extent
that it's a recipe for disaster. But rather than going in and messing with
the files manually (the mileage of which may vary depending on user
skill), why not just load everything into psfgen / NAMD ? The programs can
handle it, and with CHARMM36, we essentially eliminated the potential for
collisions.
On 10/16/2014 02:05 PM, Josh Vermaas wrote:
> Hi Francesco,
> I use psfgen built into VMD, so any legal tcl commands would work. I think
> glob and grep commands in tcl can be made to do what you want, but I'd
> strongly advocate doing the grepping manually in a terminal, and
> inspecting the residues that pop up to make sure you know what you are
> getting (protonation states, missing linkers, etc). Spending an extra
> (half?) hour of your time to look through the tree yourself will be time
> well spent if it saves you from needing to redo all your simulations
> because of a "clever" grep picked up something you didn't intend or is
> missing some important terms.
> -Josh
> On 10/16/2014 12:59 PM, Francesco Pietra wrote:
>> Hi Josh:
>>
>> 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.
>>
>> Thanks again
>> francesco
>>
>> On Wed, Oct 15, 2014 at 4:20 PM, Josh Vermaas <vermaas2_at_illinois.edu
>> <mailto: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:
>>> Hello:
>>> 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.
>>>
>>> thanks
>>> francesco pietra
>>
>>
>
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