Dear All,
I just install the modeller8v1 on SGI300 and I run the install script. At finally the message"Happy modeling!" "MODELLER Team, 2005" arise.
At the bin directory, there are such commands as mod8v1_i386-intel8,mod8v1_iris4d..... but no mod8v1. For my machine is SGI300, the command that I should use is mod8v1_iris4d. Therefore after the installation , I set the environment at the .cshrc file:
#Modeller setenv PATH $PATH://usr/people/biomd/modeller/bin setenv KEY_MODELLER8v1 xxxx(the password) alias mod8v1 mod8v1_iris4d
But when I run the examles at the automodel: run_tests
It tells me that: Fatal error, MODINSTALL8v1 environment variables not set: incomplete installation.
What is the error in my environment variables. How should I do.
-- Shulin Zhuang Chemistry Department Zhejiang University PRC shulin.zhuang@gmail.com
Let's call F(x) the Modeller objective function, which is minimized during the simulated annealing procedure. I'd like to use an alternative function to be minimized, say:
F'(x) = F(x) + k.G(x)
where F(x) is the original function, k is an arbitrary constant and G(x) is another function which can be calculated by an external program, given an intermediate model PDB file. Is there a way to accomplish this without having to edit Modeller's code? If so, how could I write a script to do this?
Lucas
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Shulin Zhuang wrote: > I just install the modeller8v1 on SGI300 and I run the install script. > At finally the message"Happy modeling!" "MODELLER Team, 2005" arise. > > At the bin directory, there are such commands as > mod8v1_i386-intel8,mod8v1_iris4d..... but no mod8v1.
If no 'mod8v1' file is produced, the installer must have encountered an error somewhere. Try running the install script again, and look carefully at the output to see if any problems are reported. You can follow this up with me directly via email rather than bothering the list.
> For my machine is SGI300, the command that I should use is > mod8v1_iris4d. Therefore after the installation , I set the environment > at the .cshrc file: > > #Modeller > setenv PATH $PATH://usr/people/biomd/modeller/bin > setenv KEY_MODELLER8v1 xxxx(the password) > alias mod8v1 mod8v1_iris4d
If you want to set the environment variables manually, you will also need to set MODINSTALL8v1 to the directory where you installed Modeller - in this case, this looks like it's /usr/people/biomd/modeller/bin
Ben Webb, Modeller Caretaker
Lucas Bleicher wrote: > Let's call F(x) the Modeller objective function, which > is minimized during the simulated annealing procedure. > I'd like to use an alternative function to be > minimized, say: > > F'(x) = F(x) + k.G(x) > > where F(x) is the original function, k is an arbitrary > constant and G(x) is another function which can be > calculated by an external program, given an > intermediate model PDB file. Is there a way to > accomplish this without having to edit Modeller's > code? If so, how could I write a script to do this?
Unfortunately there is no way to do this with Modeller 8v1. We have, however, implemented such a feature in our development version of Modeller, and it'll be one of the features of the next public release.
Note that in order for such a function to be useful during optimization, your external program must also return the first derivatives of G with respect to the Cartesian coordinates.
Ben Webb, Modeller Caretaker
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Lucas Bleicher -
Modeller Caretaker -
Shulin Zhuang