ram bio wrote:
Dear Mark,
Thanks and you are right, that when a docked complex (protein +
ligand) is simulated, the favorable ligand binding poses can be
predicted using MD (longer runs). What I am trying to do here
presently is not to simulate a docked complex, but to generate a
modelled protei
Dear Mark,
Thanks and you are right, that when a docked complex (protein +
ligand) is simulated, the favorable ligand binding poses can be
predicted using MD (longer runs). What I am trying to do here
presently is not to simulate a docked complex, but to generate a
modelled protein lowest energy c
ram bio wrote:
Dear Mark,
You mean that I should consider a configuration with the lowest total
energy for docking studies..Please clarify and suggest me.
If you read your docking program's documentation, they are using their
"energy" as a some kind of approximation to a free energy of ligand
Dear Mark,
You mean that I should consider a configuration with the lowest total
energy for docking studies..Please clarify and suggest me.
Thanks,
Ram
On Thu, Oct 22, 2009 at 3:56 AM, Mark Abraham wrote:
> ram bio wrote:
>>
>> Dear Justin,
>>
>> Thanks for the suggestion and advice.
>> As i h
ram bio wrote:
Dear Justin,
Thanks for the suggestion and advice.
As i have used a modelled protein and want to obtain the lowest energy
configuration of the protein by doing dynamics,
That's all very well, but what will that give you other than a set where
the partition of total energy into
Dear Justin,
Thanks for the advice, will try to follow using grace.
Ram
On Wed, Oct 21, 2009 at 8:25 PM, Justin A. Lemkul wrote:
>
>
> ram bio wrote:
>>
>> Dear Justin.
>>
>> Thanks for the suggestion, definitely i would run next time for a
>> longer time 2-10 ns.
>> Here, I want to learn the a
ram bio wrote:
Dear Justin.
Thanks for the suggestion, definitely i would run next time for a
longer time 2-10 ns.
Here, I want to learn the analysis part of the mdrun, In order to
locate the lowest energy frame I executed command g_energy -f
md_0_1.edr -o PE.xvg and the output was
Statistic
Dear Justin.
Thanks for the suggestion, definitely i would run next time for a
longer time 2-10 ns.
Here, I want to learn the analysis part of the mdrun, In order to
locate the lowest energy frame I executed command g_energy -f
md_0_1.edr -o PE.xvg and the output was
Statistics over 51 steps
ram bio wrote:
Dear Justin,
Thanks for the suggestion and advice.
As i have used a modelled protein and want to obtain the lowest energy
configuration of the protein by doing dynamics, i want to collect the
structure (coordinates in pdb) representing average of all the
frames/configurations pr
Dear Justin,
Thanks for the suggestion and advice.
As i have used a modelled protein and want to obtain the lowest energy
configuration of the protein by doing dynamics, i want to collect the
structure (coordinates in pdb) representing average of all the
frames/configurations produced in MD and al
ram bio wrote:
Dear Mark,
Thanks for the advice and suggestions.
I have used trjconv command as in the justin tutorial (trjconv -s
md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact),
but when i loaded the md_0_1.gro followed by md_0_1_noPBC.xtc in VMD,
i could not see the prot
Dear Mark,
Thanks for the advice and suggestions.
I have used trjconv command as in the justin tutorial (trjconv -s
md_0_1.tpr -f md_0_1.xtc -o md_0_1_noPBC.xtc -pbc mol -ur compact),
but when i loaded the md_0_1.gro followed by md_0_1_noPBC.xtc in VMD,
i could not see the protein jumping out of
ram bio wrote:
Dear Gromacs Users,
I have performed a protein in solvent simulation for 1 ns, the got the
output files as: md_0_1.cpt md_0_1.edr md_0_1.gro md_0_1.log
md_0_1.tpr md_0_1.trr md_0_1.xtc. I am following Justin Tutorial.
Can anybody tell me how to extract the coordinates ? of t
Dear Gromacs Users,
I have performed a protein in solvent simulation for 1 ns, the got the
output files as: md_0_1.cpt md_0_1.edr md_0_1.gro md_0_1.log
md_0_1.tpr md_0_1.trr md_0_1.xtc. I am following Justin Tutorial.
Can anybody tell me how to extract the coordinates ? of the simulated
prot
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