I was told before I would need to use quantum calculations to do this.
What software and method would you suggest to do this?
Thanks.
-Jonathan Saboury
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that you would
suggest to use?
Thank you for your time.
-Jonathan Saboury
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I want to simulate Iron(III) Chloride in water (in order to test some iron
sequestering agents).
I've tried to use acpype to generate an iron ion but it errors.
So I used genion and labelled the positive ion FE with charge of 3.
However grompp does not recognize the atom FE.
My question is how
I want to run a simulation of cyclohexane in deuterated chloroform.
I was able to run a sim of cyclohexane in regular chloroform, but unable to
find how to make a solvent deuterated. I know that pdb2gmx has a -heavyh
and -deuterate option, would I do it this way? It isn't a protein and would
, it is really appreciated.
-Jonathan Saboury
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That said, there is an spc.itp within the AMBER subdirectories that needs
to be
#included more explicitly, i.e. #include amber99sb.ff/spc.itp
May I ask why you are using SPC? The AMBER force fields were parametrized
with
TIP3P, so I see no viable reason to use a different water model.
Ah, fixed
Then something is wrong with the way you've done it, because the job of
spc.itp
is to define the [moleculetype] SOL and all its relevant parameters.
Hm...not sure what the matter is. Added a forcefield as well as spc.itp to
the .top file made by acpype. Still getting the error Fatal error: No
I am doing this tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html
I have set up the randomly placed cyclohexane and water throughout the box.
The problem is when i try the command grompp -f em.mdp -c biphase.gro -p
cyclohexane.top -o em.tpr it
system
(the reason I am using acpype).
Thanks again :)
- Jonathan Saboury
On Sat, Sep 21, 2013 at 12:06 PM, Jonathan Saboury jsab...@gmail.comwrote:
I am doing this tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/biphasic/index.html
I have set up
I have a Intel i7-2630QM CPU @ 2.00GHz on my laptop with 4.6.3 installed
and a desktop with an i3-3220 with 4.5.5 installed.
I am trying the same energy minimization on each of these machines. My
desktop takes a few seconds, my laptop takes hours. This doesn't make much
sense bc benchmarks
Figured out the problem. For some reason one thread is being taken up 90%
by the system. If I run it with 6 threads it runs fast. Never experienced
this on linux though, very curious.
Sorry if i wasted your time.
-Jonathan Saboury
On Fri, Sep 20, 2013 at 7:58 AM, Jonathan Saboury jsab
PDB file used :http://www.rcsb.org/pdb/explore.do?structureId=1cx2
Commands used: http://pastebin.com/raw.php?i=YYG5ad7A
Compressed folder containing all files (10.2 MB):
http://www.sendspace.com/file/rka8ei
So I want to simulate this complex. I am having problems with the .itp's
and do not know
Files: http://www.sendspace.com/file/vxcnv3
Commands used: http://pastebin.com/raw.php?i=wPqfuUwc
What I want to do: I just want to run the protein without the ligand in
explicit water. Why is the coordinate file not matching topology?
Alright, I think I have enough information now to play around with some
settings!
Thank you very much Justin, you have been very helpful :)
-Jonathan
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For the rest of us mere mortals who don't have access to specialized hardware
that allows for 10- or 20-microsecond simulations, the brute force approach is
rather futile. Techniques like steered MD and Hamiltonian replica exchange MD
are probably more feasible. Unbiased simulations of
In an implicit, non-periodic system, it is more likely that the ligand
will
float away from the protein. I've tried it and that's all that ever
happens.
Moreover, the current Gromacs version does not support implicit solvent on
GPU
and the previous version that did had very limited functionality.
Yep, the pdf was not written or copy and pasted the - incorrectly.
Thanks :)
-Jonathan
On Fri, Jul 12, 2013 at 3:03 PM, Jonathan Saboury jsab...@gmail.com wrote:
I am following Tutorial 1 from
https://extras.csc.fi/chem/courses/gmx2007/tutorial1/index.html
I try the command editconf –f
I just finished this tutorial and found it very informative:
http://cinjweb.umdnj.edu/~kerrigje/pdf_files/trp_drug_tutor.pdf
However, This was based on a complex from a pdb.
I was wondering if it was possible to just simulate the protein without
complex and put the ligand as a solute and
I am following Tutorial 1 from
https://extras.csc.fi/chem/courses/gmx2007/tutorial1/index.html
I try the command editconf –f conf.gro –bt dodecahedron –d 0.5 –o box.gro
but I get the error:
Program editconf, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/gmxlib/statutil.c, line:
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