Hello everyone,
I need avogadro to perform minimization and some other operations on
proteins. We installed avogadro on quarry which is a super computer at IU.
In quarry we cant see the interface (graphics), we can only work with the
scripts and commands. For other softwares like VMD for example
Hello David,
I thought since avogadro has python extension we can write scripts in
python and run them. I tried to execute a python script like that but the
problem is I cant turn off the graphics in avogadro. I will look into
openbabel and see if it does everything we need.
Thank you,
Divya
On
Hello Marcus, the problem we are facing is that we need to run scripts on
many molecules and we thought writing a script in python which would loop
through all the molecules would really help us but what happened is we
installed avogadro on a machine which cant bring up the graphic mode
Hi All,
Ray here. If it helps, I am a reasonably competent programmer. I
can apply
patches/code changes if they might be needed.
Ray
On 3/13/2012 11:27 AM, Divya Neelagiri wrote:
Hello everyone,
I need avogadro to perform minimization and some
Hi Divya,
On Tue, Mar 13, 2012 at 11:27 AM, Divya Neelagiri divne...@umail.iu.edu wrote:
I need avogadro to perform minimization and some other operations on
proteins.
I'm not sure how you would perform any operations without the GUI, as
there is no real command line interface to Avogadro. I
On Tue, Mar 13, 2012 at 12:26 PM, David Lonie lonieda...@gmail.com wrote:
Hi Divya,
On Tue, Mar 13, 2012 at 11:27 AM, Divya Neelagiri divne...@umail.iu.edu
wrote:
I need avogadro to perform minimization and some other operations on
proteins.
I'm not sure how you would perform any
Hi Divya,
OpenBabel became part of your environment when you added the
Avogadro SoftEnv key I sent to you. We use PBS (Torque actually)
with a Maui Scheduler on top. It is much easier than Big Red's LoadLeveler.
You can add -I to your qsub command. When your job starts, you
have an interactive
On Fri, Mar 9, 2012 at 1:28 PM, Ray Sheppard rshep...@indiana.edu wrote:
Hello Avogadro Development folks,
I recently installed Avogadro on a supercomputer for the School of
Pharmacology.
These machines work within a batch job environment. I was asked:
can you please tell me the command
Why not use Gamess (US)? Avogadro can create an inputfile for
Gamess. Gamess (and cfour) run on clusters.
sincerely,
Thorsten
On Fri, Mar 9, 2012 at 1:28 PM, Ray Sheppard rshep...@indiana.edu wrote:
Hello Avogadro Development folks,
I
Hi Dave, Thorsten,
Please meet Divya. Hi Divya. Divya is the researcher in the School
of Pharmacology
who is taking the lead in this project. I am just an old physicist that
got pressed into
supercomputer duty about 30 years ago and hasn't figured out how to
escape yet :)
Divya can
Hello Avogadro Development folks,
I recently installed Avogadro on a supercomputer for the School of
Pharmacology.
These machines work within a batch job environment. I was asked:
can you please tell me the command to execute avogadro without graphics?
I am just an old physicist that tries
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