[gmx-users] g_dyndom

[Ruben Martinez Buey]

Hi David,
Thanks a lot for your reply!!

Dyndom tells that there are three domains, and the residue numbers of each
one.
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

Any idea??
Thanks a lot
Ruben


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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