Hi,
You can try swissparam online tool to generate protein and ligand
topologies..
Cheers,
Nitin
On Wed, Nov 16, 2011 at 7:03 AM, arun kumar arunjones.kuma...@gmail.comwrote:
hi justin,
as u said i understand that there is inconsistency in the charges and
charge groups of PRODRG server
Thanks. But in timeline plugin of VMD I am able to measure RMSD with
respect to one of the frame of trajectory and I am interested to measure
RMSD with respect to another molecule. I am trying to measure RMSD of
trajectory frames with respect to Bound and unbound configuration of
molecule so that
Hi arun,
You can try swissparam online tool to generate protein and ligand
topologies..
Cheers,
Nitin
--
Sainitin D
PhD student
Bioinformatics Group
Biotechnology Center
Technische Universität Dresden
Tatzberg 47/49
01307 Dresden, Germany
Tel Lab:+49 (0)351 463 40060
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gmx-users mailing
Hi GMX Users,
I am doing Justin tutorial of Umbrella sampling. I have just finished
continous pulling of chainA from the reference chainB. I have some
questions. I looked at the trajectory of pulling and it has began with
dissociating residue 27Alanine from the ChainB following 26, 25, 24...1. My
Please do not include the entire digest in your post. The archive becomes
hopelessly confusing when this happens...
arun kumar wrote:
hi justin,
as u said i understand that there is inconsistency in the charges and
charge groups of PRODRG server itself.
can u suggest me any other
shilpa yadahalli wrote:
Dear Justin,
sorry to trouble you again. I want to ask one more thing.
I saw some of the documentation regarding, and i found that (on d page u
mentioned frm gromacs), for a box of 216 waters, fluctuations of 500-600
bar are standard. And for a system of 21600 water
Hi,
What is the relation between pulling force and free energy of binding. can
we relate the maximum pulling force with the free energy. for example, 2
systems has the maximum pulling force and free energy as below from
umbrella sampling and g_wham analysis,
max. force
Vijayaraj wrote:
Hi,
What is the relation between pulling force and free energy of binding.
can we relate the maximum pulling force with the free energy. for
example, 2 systems has the maximum pulling force and free energy as
below from umbrella sampling and g_wham analysis,
Steven Neumann wrote:
Hi GMX Users,
I am doing Justin tutorial of Umbrella sampling. I have just finished
continous pulling of chainA from the reference chainB. I have some
questions. I looked at the trajectory of pulling and it has began with
dissociating residue 27Alanine from the
Thank you Justin, now I get what you mean!
As I understood I should pick just one frame untill 189 ps (when
dissociation occured) - does it matter which one I will choose on the final
binding free energy?
Then spacing should be 0.2 nm. Right? But how is it possible to do spacing
like this from
Steven Neumann wrote:
Thank you Justin, now I get what you mean!
As I understood I should pick just one frame untill 189 ps (when
dissociation occured) - does it matter which one I will choose on the
final binding free energy?
The free energy minimum should (theoretically) be when the
Thank you Justin! That helped a lot!
Steven
On Wed, Nov 16, 2011 at 3:06 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Steven Neumann wrote:
Thank you Justin, now I get what you mean!
As I understood I should pick just one frame untill 189 ps (when
dissociation occured) - does it matter
Message: 4
Date: Wed, 16 Nov 2011 09:34:02 -0500
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] pulling force vs free energy
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID: 4ec3c9da.7040...@vt.edu
Content-Type: text/plain; charset=ISO-8859-1;
Vijayaraj wrote:
Message: 4
Date: Wed, 16 Nov 2011 09:34:02 -0500
From: Justin A. Lemkul jalem...@vt.edu mailto:jalem...@vt.edu
Subject: Re: [gmx-users] pulling force vs free energy
To: Discussion list for GROMACS users gmx-users@gromacs.org
Dear all,
I am wondering if there is a way to calculate the potential of a given RNA
structure? No minimization, no simulation, but calculate the potential.
--
Best,
Liang Liu
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Please search
I agree with Justin. I have tried myself several SMD simulations for ligand
binding studies. I tried 500 simulations and not sure if they are enough.
Further, the path dependence is very important part.
For different paths that you can try, look at McCammon group's paper in
JACS 128, 3019-3026.
Liu, Liang wrote:
Dear all,
I am wondering if there is a way to calculate the potential of a given
RNA structure? No minimization, no simulation, but calculate the potential.
You can do a single-point energy evaluation with the md integrator and nsteps
set to 0.
-Justin
--
Hi, all
I just restart a simulation with 'mpirun -np 8 mdrun -pd yes -s md_0_1.tpr -cpi
state.cpt -append'
However, the following error appears:
Output file appending has been requested,
but some output files listed in the checkpoint file state.cpt
are not present or are named differently by
*** Deadline Extended to December 6, 2011 ***
** Please submit your abstract before November 25, 2011 *
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CALL FOR PAPERS
2nd International Workshop
Hi,
I was running a simulation of 10ns which crashed in between at 1.7 ns due
to power failure. I used the following command to restart the simulation
form that point:
mdrun -s topol.tpr -cpi state.cpt -append
After checking the file md_0_1.log and others , I am getting data only for
those
On Wed, Nov 16, 2011 at 4:11 PM, xianqiang xianqiang...@126.com wrote:
Hi, all
I just restart a simulation with 'mpirun -np 8 mdrun -pd yes -s md_0_1.tpr
-cpi state.cpt -append'
However, the following error appears:
Output file appending has been requested,
but some output files
On Wed, Nov 16, 2011 at 7:57 PM, bharat gupta bharat.85.m...@gmail.comwrote:
Hi,
I was running a simulation of 10ns which crashed in between at 1.7 ns
due to power failure. I used the following command to restart the
simulation form that point:
mdrun -s topol.tpr -cpi state.cpt -append
Greeting
i looking for residues forming Hydrogen bonds with one residue,i can't get
that.
When using -hbm i get an xpm file that contain existence of hbond over time
without any indication about who's the other residues.(it is just binary
existence)
is there a way to get residues engaged in the
larif sofiene wrote:
Greeting
i looking for residues forming Hydrogen bonds with one residue,i can't
get that.
Have you tried using an index group that specifies the residue of interest?
When using -hbm i get an xpm file that contain existence of hbond over
time without any indication
Greeting
i looking for residues forming Hydrogen bonds with one residue,i can't
get that.
When using -hbm i get an xpm file that contain existence of hbond over
time without any indication about who's the other residues.(it is just
binary existence)
You can check the bonds index created by
Hi,
I was running a simulation of 10ns which crashed in between at 1.7 ns due
to power failure. I used the following command to restart the simulation
form that point:
mdrun -s topol.tpr -cpi state.cpt -append
After checking the file md_0_1.log and others , I am getting data only for
those
On 16/11/2011 5:02 PM, Harpreet Basra wrote:
Hi Mark,
Sorry my last mail was incomplete...here is the complete one!
On 16/11/2011 1:18 AM, Harpreet Basra wrote:
Hi Mark,
Thanks for the quick reply. But i have already done what u
suggested.
On
On 16/11/2011 5:00 AM, Liu, Liang wrote:
The tabulated potentials I am using is non-bonded interactions. The
question is the application of these potentials will only modify the
force field, e.g. amber03, or will take place of the force field?
The force field is more than the non-bonded
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