Re: [AMBER] forefield for Pyridoxal 5-phosphate

From: FyD <fyd.q4md-forcefieldtools.org>
Date: Fri, 12 Oct 2012 22:02:08 +0200

Dear BALA SUBRAMANI,

> could anyine tell me how to generate forcefield files (frcmod, prep, lib
> files) for Pyridoxal 5-phosphate (mol. formula C8H10NO6P). I have tried all
> the options available in amber, still it was showing some errors. please tell
> me guys, how to fix this problem.

Starting from:
  http://en.wikipedia.org/wiki/Pyridoxal_phosphate

See http://q4md-forcefieldtools.org/REDS/
     http://q4md-forcefieldtools.org/REDS/faq.php#22
  then
http://q4mdfft:q4mdfft2012.cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFlIGoUrUSADFT31wDADFZQ4mPKhvlDllygsADF/P413.html
  &
http://q4mdfft:q4mdfft2012.cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFlIGoUrUSADFT31wDADFZQ4mPKhvlDllygsADF/P413/javaappletmol2-1.html
  &
http://q4mdfft:q4mdfft2012.cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFlIGoUrUSADFT31wDADFZQ4mPKhvlDllygsADF/P413/Data-R.E.D.Server/
  &
http://q4mdfft:q4mdfft2012.cluster.q4md-forcefieldtools.org/~ucpublic1/ADF1ADFlIGoUrUSADFT31wDADFZQ4mPKhvlDllygsADF/P413/Data-R.E.D.Server/Mol_m1-o1.mol2

this took : "Execution time: 0 h 8 m 45 s" on the server.

I would split this molecule into two parts: the aromatic ring & the
phosphate; anyway you have a first starting point/example...

regards, Francois



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Received on Fri Oct 12 2012 - 13:30:03 PDT