Problem including substrate and heme
I am wondering what the format is for input in the alignment file of two molecules say heme (h) and myristic acid (5) distinct from the protein of interest.
My guess is:
AATLCLL(protein sequence)GT/h/5*
The order they appear in the pdb file is AA/heme/myristate.
Is this the format? When I use it the myristic acid input is ignored.
Jeff
-- Jeffrey P. Jones, Ph.D. Associate Professor of Pharmacology, Physiology Biochemistry and Biophysics (716)275-5371, http://cyp.medicine.rochester.edu/~jpj/jones_group.html jpj@cyp.medicine.rochester.edu
Hi, Jeffrey!
Jeffrey P. Jones wrote: > > I am wondering what the format is for input in the alignment file of two > molecules say heme (h) and myristic acid (5) distinct from the protein > of interest. > > My guess is: > > AATLCLL(protein sequence)GT/h/5*
Please read the corresponding example in FAQ in the manual, how to deal with small molecules of non-aminoacid nature.
The format is oK, but you have to specify in some library file what h and 5 is (Hem is probably present in the standard library).
Yours, Azat.
> > The order they appear in the pdb file is AA/heme/myristate. > > Is this the format? When I use it the myristic acid input is ignored. > > Jeff > > -- > Jeffrey P. Jones, Ph.D. > Associate Professor of Pharmacology, Physiology > Biochemistry and Biophysics > (716)275-5371, http://cyp.medicine.rochester.edu/~jpj/jones_group.html > jpj@cyp.medicine.rochester.edu
-- - Dr. Azat Badretdinov - The Rockefeller Univ, Box 270 - 1230 York Ave, New York NY 10021, USA - Phone: (212) 327 7206 - Fax: (212) 327 7540 - E-mail: azat@salilab.org - WWW/URL: http://salilab.org/~azat
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Azat Badretdinov -
Jeffrey P. Jones