Hi Thripthi,
I would suggest that you check a few things:
- when defining the gridbox coordinates, did you set the spacing to 1?
- did you properly prepare your receptor (remove bound ligands, ions,
waters, adding missing residues to your structure etc) and add polar
hydrogens?
-
You can also map conservation with VMD, if memory serves (have not done
this in quite a while).
On Thu, Jan 4, 2024 at 9:34 AM Roberto Steiner <
2497b6493202-dmarc-requ...@jiscmail.ac.uk> wrote:
> ConservFold from the Rodrigues lab at Warwick is something that you might
> consider.
>
It is most likely the spacing setting in PMV (it is set to the default
value used by the original Autodock, namely 0.375A). In Autodock Vina it
should be set to 1 angstrom.
Let me know if this helps
Kind regards,
Sorin
On Sun, Nov 19, 2023 at 1:57 PM BRUNO DI GERONIMO QUINTERO <
Hi Lucky,
GROMACS can do mixed solvent MD simulations quite easily
On Mon, Nov 15, 2021 at 11:30 AM 卢宏运 wrote:
> Dear All,
>
> I was wondering if there is a skilled software to simulate the structural
> changes of proteins at different organic solvent?
>
>
> regards,
> Lucky
>
>
>
>
>
>
Hello Domen,
If you are based in Europe, I recommend checking out Tuxedo laptops, which
you can customize based on budget and preference - I've recently got a
Ryzen 3950x with a RTX2070 to run heavy computational work and it does the
job quite well. The downside is that their customer support is
nce you want data on the free and bound forms of the
> complex) at 0.5 - 1 mM depending upon the size of the molecule which
> relates to the complexity of the NMR spectrum due to number of resonances
> and the relaxation times. The total volume required for each sample is
> betwe
depends upon the size of the molecule.
> You will need at least 2-3 samples that are differentially labeled with
> 15N, 13C (also since you want data on the free and bound forms of the
> complex) at 0.5 - 1 mM depending upon the size of the molecule which
> relates to the complexity of the N
ers, Jon.C.
>
>
> Sent from ProtonMail mobile
>
>
>
> ---- Original Message
> On 15 Aug 2021, 09:16, Sorin Draga < sor.dr...@gmail.com> wrote:
>
>
> Hello Ethan,
>
> Thank you for the suggestions. I should have mentioned in my initial post
> that my intention i
ProtonMail mobile
>
>
>
> Original Message
> On 15 Aug 2021, 09:16, Sorin Draga < sor.dr...@gmail.com> wrote:
>
>
> Hello Ethan,
>
> Thank you for the suggestions. I should have mentioned in my initial post
> that my intention is to first conduct a hi
should be well within its scope.
>
> best
>
> Ethan
>
> On Saturday, 14 August 2021 14:12:40 PDT Sorin Draga wrote:
> > Hello everyone,
> >
> > I do realize that this is not a NMR focused group, but I do hope that
> there
> > are
Hello everyone,
I do realize that this is not a NMR focused group, but I do hope that there
are a few spectroscopists lurking around that could possibly answer a few
questions (I am more of a modeler/computationalist):
The problem: I have two intrinsically disordered proteins that are known to
Hello everyone,
While this is not exactly a crystallography question, I do think that most
of you are well versed in structural analysis.
The problem: I have a very large number of ligands (>100.000) resulting
from blind docking against a certain receptor. Due to the large number,
this can not be
I am not sure what you mean by polymer formation. Presuming that you have
optimized your protein concentration, pH and salt concentration, you could
try arginine as an anti-aggregation agent in your purification (I presume
you do FPLC). Have a look at chaotropic agents used in protein
Dear Andre,
I am not sure what you mean by conformational space around the model, but
to answer your question: short energy minimization can be done using, for
example, deep view/swiss pdb viewer. However, I think that you are most
likely looking for a short bout of molecular dynamics, in which
ionate into another
> well. Use the time as base and keep the Äkta pumping at constant speed.
> Curious if someone knows a better strategy!
> Best, matthias
>
> ------
> *From:* CCP4 bulletin board on behalf of Sorin
> Draga
> *Sent:* Monday, June 3, 20
Dear all,
We have an old akta system, running Unicorn 4.0, recently donated to our
lab. While attempting to fractionate a protein mixture, I was unable to
convince Unicorn to fractionate within given limits (say, for ex peak A
between RT a and b and peak B between retention times c and d). All
the closest thing I can think of is tetramer of hAQP4
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2678640/
On Wed, Jun 27, 2018 at 2:07 PM, david lawson (JIC)
wrote:
> Hi All
>
>
>
> Apologies for the off-topic question.
>
>
>
> The attached image has been hanging on the wall at our
17 matches
Mail list logo
