Ruben Martinez Buey
ruben at akilonia.cib.csic.es
Fri Dec 20 01:15:30 CET 2002
Thanks a lot for your reply!!
Dyndom tells that there are three domains, and the residue numbers of each
I specify this domains in the index file and run g_dyndom:
Select group to rotate:
Group 0 ( System) has 2553 elements
Group 1 ( Protein) has 2553 elements
Group 2 ( Protein-H) has 2553 elements
Group 3 ( C-alpha) has 408 elements
Group 4 ( Backbone) has 1076 elements
Group 5 ( MainChain) has 1410 elements
Group 6 (MainChain+Cb) has 1711 elements
Group 7 ( MainChain+H) has 1410 elements
Group 8 ( SideChain) has 1143 elements
Group 9 ( SideChain-H) has 1143 elements
Group 10 ( domain1) has 1170 elements
Group 11 ( domain2) has 160 elements
Group 12 ( domain3) has 651 elements
Select a group: 12
Going to rotate Protein-H containg 2553 atoms
Back Off! I just backed up rotated.xtc to ./#rotated.xtc.1#
Frame: 0 (label A), angle: 0.000 deg., trans: nan0x7ffffe00 nm
Fatal error: Arrow vector not given
Thanks a lot
David van der Spoel wrote:
> On Thu, 2002-12-19 at 20:39, Ruben Martinez Buey wrote:
> > Hi all,
> > I am trying to run g_dyndom but I cannot get it!!
> > What are the input files for g_gyndom??
> > -f .... the output pdb file from dyndom called mi-title_pdb??
> > -n .... What file is it?? Is it another output file from dyndom? which?
> index file is to separate which doman is whioch. you have to make it
> yourself. maybe check how dyndom separates the domains. if it is by a
> chain label you can use that in make_ndx
> Groeten, David.
> Dr. David van der Spoel, Biomedical center, Dept. of Biochemistry
> Husargatan 3, Box 576, 75123 Uppsala, Sweden
> phone: 46 18 471 4205 fax: 46 18 511 755
> spoel at xray.bmc.uu.se spoel at gromacs.org http://xray.bmc.uu.se/~spoel
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