gupta wrote:
Thanks for your advice... Could you please refer me some papers
regarding this
On Sat, Dec 31, 2011 at 8:17 AM, KS Rotondi
wrote:
No, there is no way to use such data to determine the folding rate
of the intact protein. If you used a fragment approach you could
potent
Dear Bharat,
20 residue peptides in general don't fold, they inhabit a
conformational space. Can you determine the fraction of time spent in
a near native (as defined by you) conformation under given conditions
to within the ability of the force field, yes, you can. To calculate a
true ra
No, there is no way to use such data to determine the folding rate of
the intact protein. If you used a fragment approach you could
potentially (read lots of papers on REMD) isolate nucleation sites,
but minus the tertiary interaction scheme you could not tell a
compelling story. Now, if yo
you either
A) Have not been sampling long enough
or
B) Just might have your answer...
On Oct 10, 2011, at 11:46 AM, Liu, Liang wrote:
Well, the thing is even I turn off the position restraint and raise
the temperature to 600k, the RMSD I can obtained is only about 0.3
for a RNA hairpin. -
thumbs up per tuti
On Jul 15, 2011, at 6:23 PM, Justin A. Lemkul wrote:
Sara baretller wrote:
between 2.2 and 2.7 M.
Well, double check your work. Your previous post contained several
units that made no sense, so I don't know if you've done the
calculations correctly. For adding ions,
complete commitment to help on Justin's part.
KSR
On Sep 12, 2010, at 6:27 PM, KS Rotondi wrote:
it must be hard to do your own research
On Sep 12, 2010, at 5:52 PM, manoj singh wrote:
Thanks for reminding me the existence of Google.
It must be hard to copy and paste few lines of the PBS s
it must be hard to do your own research
On Sep 12, 2010, at 5:52 PM, manoj singh wrote:
Thanks for reminding me the existence of Google.
It must be hard to copy and paste few lines of the PBS script than
advertising the Google.
On Sun, Sep 12, 2010 at 5:23 PM, Justin A. Lemkul
wrote:
m
The link takes me to the Tab Potentials page, but using the latest
Firefox with Mac OS 10.5.8 there are gaps in the text but no functions
shown at the top of the page. E.g. generic form is: several blank
lines, LJ form is: even more blank lines, etc.
On Aug 24, 2010, at 3:48 PM, Justin A
I'm joining the tautology society as well... : ) The by-line is, "if
we get 100,000 members, we'll have 100,000 members..."
On Feb 20, 2010, at 4:28 PM, Tsjerk Wassenaar wrote:
Aside from that, search the literature; published papers should have
reproducible methodology :)
And.., methodology
This question came up a few weeks ago.
The simple answer is, you can be pretty sure you're at the bottom of
some potential energy surface but you can't know if you're at a local
or global minimum.
However, if you are using an experimentally determined protein
structure, and the structure
Many thanks to Mr. Lemkul and Mr. Rodrigues, their solution was, as
they say, the ticket.
Ken
On Apr 3, 2009, at 1:57 PM, Justin A. Lemkul wrote:
KS Rotondi wrote:
All, I've looked at the site and cannot figure this out, so
apologies if this is a painful often seen question. I
All,
I've looked at the site and cannot figure this out, so apologies if
this is a painful often seen question.
I'm trying to install dssp for use with do_dssp on an OSX.5 PPC system
with the following steps, in the dssp folder:
./DsspCompileCC
cd..
sudo mv dssp /usr/local
cd /usr/loca
Dearest All,
I'm experiencing strange behavior running Gromacs 4.0.2 on dual G5
macintoshs (OS 10.4.11) in my college's computer laboratory. When I
use the attached .mdp file, grompp ends in a seg fault, however if I
remove the last 3 lines (controlling velocity generation) grompp runs
n
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