I am trying to differentiate between several binding poses for a protein
ligand complex.
Initially I tried the LIE method however its results do not followed the
expected trend based on experimental data. I then looked at the raw
interaction energies between the ligand and its environment
I have been avoiding TI or FEP as I doubt my ligand parametrisation is good
enough to warrant the effort. What I am trying to do is get a rough method
working as a secondary screen in a lead optimisation effort. I am not trying
to be perfect, I am just trying to be better than docking at this
as LIG-rest?
All the best,
Tom
On 14/08/2012 11:07 AM, Tom Dupree wrote:
Greetings all,
Can I easily obtain the potential energy for a energy group rather than the
whole simulation cell?
Yes. See manual 3.3 and 7.3.8. But below you imply you're already doing this.
You can make custom groups
PME has a reciprocal component of the energy that cannot be calculated for each
individual atom. Hence it can't be assigned to an energy group (at least that
is my understanding).
I just use RF-0 to rerun the trajectory using a much larger cut off to try and
account for the errors that way. At
There are different methods used to calculate the electrostatics, RF-0 is one.
7.3.10 in the manual.
You can just use the -rerun flag in mdrun, after creating an appropriate .tpr
file with grompp and a new .mdp file.
If I understand it properly this effectively calculates single point
Greetings all,
Can I easily obtain the potential energy for a energy group rather than the
whole simulation cell? Does it make any sense to do so?
I am simulating protein ligand complexes and have observed movement in some
cases. When I analyse the interaction energy sum of LJ and columbic of
You need to assign your own experimentally determined values to -Elj and -Eqq.
These are determined by simulating your ligand in a solvent box.
g_lie uses some common values found in the literature for -Clj and -Cqq again
you need to decide if they are appropriate in your case. Try reading papers
Greetings all,
I can't manually reproduce g_lie results.
After raging at excel for a while I think I have found a bug.
Here is my first time point,
Reported by g_lie to be 35.0073
From energy file
Lj_complex =-130.762
Coul_complex = -286.746
My constants specified to g_lie
Clj = Alpha = lj_const
, and the second last time point has different
values. This is a single run so I don't think I should have concatenation
issues?
I just checked the counts and there are 476 time points in the energy file and
477 in the g_lie file.
All the best,
Tom
On 14/06/2012 3:56 PM, Tom Dupree wrote:
Greetings all,
I
to build the .tpr
file?
All the best,
Tom
___
Message: 2
Date: Mon, 21 May 2012 03:26:07 +
From: Tom Dupree t.dup...@unsw.edu.au
Subject: [gmx-users] LIE methodology check (mdrun -rerun cutoffs and
box vectors)
To: gmx-users@gromacs.org gmx
Greetings all,
Background:
I have a series of MD runs of a protein ligand complex where I have used PME,
they represent far more calculations than I have time to repeat in full. I
recently became aware that the coulombic interaction energy reported when PME
is used is not valid for use with
Greetings all,
I am quite interested in this discussion, and wondered if some people would
like to add how they would assess the length their MD simulations. I am
currently simulating HIV-1 RT for 1 ns and seem to have very flat energy
profiles for almost anything (energy wise) I care to
Greetings all,
I have run into a little bit of a problem.
I am trying to simulate a hetro-dimer. Through previous work we have identified
302 C-alphas (of 960 odd residues) that don't move much. Previously we
position restrained these atoms in our simulations using charmm which gave us a
Greetings all,
I am new to Linux and wish to confirm some facts before I press on with the
installation.
In the installation guide,
http://www.gromacs.org/Downloads/Installation_Instructions
There is a line saying ...Where assembly loops are in use, GROMACS
performance is largely
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