[gmx-users] indexing and new molecules

Itamar Kass Itamar.Kass at med.monash.edu.au
Tue Feb 16 05:06:03 CET 2010

Shalom all,

I am simulating a protein in which one of the residues is chemically
modified (non-natural) - so I had to add it into aminoacids.dat.

I found that when I analyse my results, and use the index group of the
protein this amino acid does not count unless the aminoacids.dat file is
available in the same folder.

Now, I don't think this is a bug - it is perfectly logic that in order
to index the protein the program needs to know how amino acid looks
like. I just think this should be written somewhere.



"In theory, there is no difference between theory and practice. But, in
practice, there is." - Jan L.A. van de Snepscheut

| Itamar Kass, Ph.D.
| Postdoctoral Research Fellow
| Department of Biochemistry and Molecular Biology
| Building 77 Clayton Campus
| Wellington Road
| Monash University,
| Victoria 3800
| Australia
| Tel: +61 3 9902 9376
| Fax: +61 3 9902 9500
| E-mail: Itamar.Kass at med.monash.edu.au

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