[gmx-users] do_dssp for many peptides

the second half (chains M-X) produces a flawed behavior of do_dssp. Does anyone have an idea what is going wrong? Cheers, Volker -- Dr. Volker Knecht Department of Theory and Bio-Systems Max Planck Institute of Colloids and Interfaces Research Campus Golm 14424 Potsdam, Germany http://www.mpikg

[gmx-users] Re: Re: do_dssp for many peptides

denoted as chain N: do_dssp claims that are 124 residues in my selected group, although 124 is the number of *atoms* (not of residues) of this peptide. After the notion that some temporary file is backed up, do_dssp gets stuck again. Volker -- Dr. Volker Knecht Department of Theory and Bio

[gmx-users] do_dssp: main chain

in some cases. Indeed, choosing 'MainChain' (indeed index group 5) does not help, but results in the same behavior. Volker -- Dr. Volker Knecht Department of Theory and Bio-Systems Max Planck Institute of Colloids and Interfaces Research Campus Golm 14424 Potsdam, Germany http://www.mpikg

[gmx-users] epsilon_rf

, ranging from rigorous to pragmatic, coexist in the community, and it would be nice if some of you could provide their opinion. Kind regards, Volker -- Dr. Volker Knecht Department of Theory and Bio-Systems Max Planck Institute of Colloids and Interfaces Research Campus Golm 14424 Potsdam

[gmx-users] Origin of g_mindist problems located

is obtained with g_mindist if the names for the selected groups created by make_ndx are too long for complicated selections. If these automatically generated names are replaced by shorter ones manually in a text editor, the program again works fine. Cheers, Volker -- Dr. Volker Knecht Theory

[gmx-users] Bug in g_mindist version 3.3.1?

. Therefore it would very helpful if the apparent bug in version 3.3.1 could be fixed. Thanks in advance. Kind regards, Volker -- Dr. Volker Knecht Theory Department Max Planck Institute of Colloids and Interfaces Research Campus Golm 14424 Potsdam, Germany Phone: +49-331-567-9610 Fax: +49-331-567-9612