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#37618 - 08/19/19 02:59 AM Problem use gui for Chlorophyll a's part
jtyang Offline
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Registered: 05/09/17
Posts: 6
Hey guys,

My protein has some part of Chlorophyll a, say CHL and DGD ligands, and I want to use gui to generate force field I can use in charmm, but the gui crushed with no error report and no output.

I know I can use OPLS-AA ff do this, but I'd like to do work with charmm , so...it's gui's problem? or can I find charmm ff of Chlorophyll a (or CHL,DGD) elsewhere?

Thanks for any possible help

J.T.Yang

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#37619 - 08/19/19 11:35 AM Re: Problem use gui for Chlorophyll a's part [Re: jtyang]
rmv Online   content

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Registered: 09/17/03
Posts: 8373
Loc: 39 03 48 N, 77 06 54 W
J Mol Graph Model. 2015 May;58:30-9. doi: 10.1016/j.jmgm.2015.03.001 Epub 2015 Mar 10.

Revised force-field parameters for chlorophyll-a, pheophytin-a and plastoquinone-9.
Guerra F1, Adam S1, Bondar AN2.

Erratum in
J Mol Graph Model. 2015 Jun;59:129.
_________________________
Rick Venable
computational chemist


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#37620 - 08/20/19 02:56 AM Re: Problem use gui for Chlorophyll a's part [Re: jtyang]
jtyang Offline
Forum Member

Registered: 05/09/17
Posts: 6
Thanks a lot!

Actually I've seen that paper but I didn't notice the erratum, and still wonder if there is more convenient way, like packaged ff files or something, seems life is always not easy.

Again, thanks for your reply.

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#37621 - 08/20/19 10:52 AM Re: Problem use gui for Chlorophyll a's part [Re: jtyang]
rmv Online   content

Forum Member

Registered: 09/17/03
Posts: 8373
Loc: 39 03 48 N, 77 06 54 W
I have not used these parameters, but they appear to be a reasonable starting point.
_________________________
Rick Venable
computational chemist


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