The problem is that there is no MYR entry in the top_heav.lib or other top*.lib libraries in the standard distribution. Please check all the times that the entry of the molecule is present in BOTH restyp.lib and top*.lib corresponding to your model (all atoms, heavy atoms only, etc.).

Azat.

Jeffrey P. Jones wrote: > > Thanks for your reply. Both of these residues are in the library files, h & 5 > are the default single letter descriptors. Any other suggestions? > > Azat Badretdinov wrote: > > > 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 > > -- > 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