Thank you..
On Wed, Nov 6, 2013 at 7:39 PM, Justin Lemkul wrote:
>
>
> On 11/6/13 5:47 AM, Kavyashree M wrote:
>
>> Dear users,
>>
>> Sorry for repeating the same question. I just wanted to know
>> whether is it ok if I have rlist > rcoulomb in ligand-water and
>> prot-lig-water rerun md (wi
On 11/6/13 5:47 AM, Kavyashree M wrote:
Dear users,
Sorry for repeating the same question. I just wanted to know
whether is it ok if I have rlist > rcoulomb in ligand-water and
prot-lig-water rerun md (with RF-0) while having rlist = rcoulomb
in the original simulation using PME?
The energi
Dear users,
Sorry for repeating the same question. I just wanted to know
whether is it ok if I have rlist > rcoulomb in ligand-water and
prot-lig-water rerun md (with RF-0) while having rlist = rcoulomb
in the original simulation using PME?
Thank you
Regards
Kavya
On Wed, Nov 6, 2013 at 11
Dear users,
When the simulation was carried out with PME
rcoulomb was set equal to rlist. But when I need to
to ligand-water simulation without PME (with RF-0)
then it requires rlist greater by 0.1-0.3 than rcoulomb.
So if I rerun protein-ligand-water simulation there
could be more differences in
On 11/4/13 1:52 AM, Saman Shahriyari wrote:
dear gmx users
i am trying to use g_lie tool regarding the fact i am a
newbie to this. so i searched through the web for an appropriate
protocol. although there are lots of staffs discussing the theory, but i
couldn't find any thing describing the
dear gmx users
i am trying to use g_lie tool regarding the fact i am a
newbie to this. so i searched through the web for an appropriate
protocol. although there are lots of staffs discussing the theory, but i
couldn't find any thing describing the steps techniqally and with some
details.
genera
Ok thank you. I thought it was for protein-ligand-water
that needs to be rerun without PME.
Thanks
Regards
Kavya
On Sat, Nov 2, 2013 at 9:45 PM, Justin Lemkul wrote:
>
>
> On 11/2/13 12:14 PM, Kavyashree M wrote:
>
>> Sir,
>>
>> Thank you. Should the ligand-water MD be done without PME?
>>
>>
On 11/2/13 12:14 PM, Kavyashree M wrote:
Sir,
Thank you. Should the ligand-water MD be done without PME?
I already answered this. Please read my previous reply again.
-Justin
Thank you
Regards
Kavya
On Sat, Nov 2, 2013 at 9:13 PM, Justin Lemkul wrote:
On 11/2/13 1:22 AM, Kavyash
Sir,
Thank you. Should the ligand-water MD be done without PME?
Thank you
Regards
Kavya
On Sat, Nov 2, 2013 at 9:13 PM, Justin Lemkul wrote:
>
>
> On 11/2/13 1:22 AM, Kavyashree M wrote:
>
>> Dear Users,
>>
>> Its mentioned in the list that it would be
>> wrong to use g_lie on a simulation w
On 11/2/13 1:22 AM, Kavyashree M wrote:
Dear Users,
Its mentioned in the list that it would be
wrong to use g_lie on a simulation which
uses PME.
So kindly suggest any other way available
to get the free energy of ligand binding other
using g_lie?
The original simulation should be done wit
On 11/2/13 1:00 AM, Kavyashree M wrote:
Dear Gromacs users,
I have a protein-ligand in water simulation (Gmx 4.5.3), for
calculating free energy of ligand binding, a separate simulation
of ligand in water simulation is required (which I read from the
list). The question is the protein-ligand i
Dear Users,
Its mentioned in the list that it would be
wrong to use g_lie on a simulation which
uses PME.
So kindly suggest any other way available
to get the free energy of ligand binding other
using g_lie?
Thank you
Regards
kavya
--
gmx-users mailing listgmx-users@gromacs.org
http://lists
Dear Gromacs users,
I have a protein-ligand in water simulation (Gmx 4.5.3), for
calculating free energy of ligand binding, a separate simulation
of ligand in water simulation is required (which I read from the
list). The question is the protein-ligand is simulated as a dimeric
system so is it nec
hi
must all mdp files be similar for g_lie program? shouldn't i use of PME in all
mdp files?
what edr file must i use as input file for g_lie?
many thanks
/
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please s
On 14/06/2012 3:56 PM, Tom Dupree wrote:
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 constant
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
I am trying to figure out how to use the g_lie tool in gromacs. I have the
dGbind value for the ligand-solvent interactions and for the protein-ligand
complex.
However, I cannot find in the manual what units these values are. I get the
following:
DGbind = 1953867.080 (0.664)
and
DGbind = 185147
Hi all,
Could anyone please refer to me to a paper or other resource that explains
in detail (specifically technical) on how to preform g_lie. I know the
matter has been brought up here quit often lately but looking through the
mailing list archives and reference papaers (Aquist et al. and similar
Greetings to all!
I have a question for the g_lie function users...
Is there anyone who used this function successfully including the -Elj and -Eqq
options???
When I'm trying to use this function with the above mentioned options I'm
getting Zeros for both Elj and Eqq
or any other value w
g_lie calculates the deltaG= alpha(p - w) + beta(p - w) equation. But when calculating DGbind from g_lie it will
ask for only one term at a time i.e. -Elj for either p or w and -Cqq for either p or w. My question is when
using only p for -Elj and Vl-s el>p for -Cqq, how the LJ and EL
terms calcul
Anirban Ghosh wrote:
Thanks Justin.
Yes I did use PME during the simulations. But still when I process the
.edr file with g_energy, it gives both the options...LJ-1-4 and LJ(SR).
So if I am not wrong, I should be using the LJ(SR) value as the Elj in
the LIE calculation. Right?
I'll have
Thanks Justin.
Yes I did use PME during the simulations. But still when I process the .edr
file with g_energy, it gives both the options...LJ-1-4 and LJ(SR). So if I
am not wrong, I should be using the LJ(SR) value as the Elj in the LIE
calculation. Right?
Thanks again.
Anirban
On Tue, Dec 28,
Anirban Ghosh wrote:
Thanks a lot Justin for the reply !!!
While calculating the Elj and Eqq values should we consider the
short-ranged LJ (LJ-SR) or LJ-14, the two components that are present in
1-4 interactions are intramolecular, thus should not be relevant to the LIE
calculation.
t
Thanks a lot Justin for the reply !!!
While calculating the Elj and Eqq values should we consider the short-ranged
LJ (LJ-SR) or LJ-14, the two components that are present in the .edr file?
And for Coulomb also?
Which one should we consider?
Thanks again.
Anirban
On Tue, Dec 28, 2010 at 11:03
Thanks a lot Justin !!!
--Anirban
On Tue, Dec 28, 2010 at 11:03 PM, Justin A. Lemkul wrote:
>
>
> Anirban Ghosh wrote:
>
>> Thanks a lot Justin for the reply.
>> Yes I am going through all the relevant literature on LIE.
>> Actually the lie.xvg file contains the same value of -25.4 for all the
Anirban Ghosh wrote:
Thanks a lot Justin for the reply.
Yes I am going through all the relevant literature on LIE.
Actually the lie.xvg file contains the same value of -25.4 for all the
frames. So I am getting a straight line plot. Why is this happening? Am
I missing out something?
If the
Thanks a lot Justin for the reply.
Yes I am going through all the relevant literature on LIE.
Actually the lie.xvg file contains the same value of -25.4 for all the
frames. So I am getting a straight line plot. Why is this happening? Am I
missing out something?
Thanks a lot again.
Anirban
On Tu
Anirban Ghosh wrote:
Thanks a lot Justin for the reply.
So I ran a simulation with my ligand in water for 1 ns and using
g_energy I calculated the LG-14 and Coulomb-14 values from the .edr
file. I supplied the average of these two values as my Elj and Eqq to
g_lie and I got the DGbind as -25
Thanks a lot Justin for the reply.
So I ran a simulation with my ligand in water for 1 ns and using g_energy I
calculated the LG-14 and Coulomb-14 values from the .edr file. I supplied
the average of these two values as my Elj and Eqq to g_lie and I got the
DGbind as -25.4. Is this the correct way
Anirban Ghosh wrote:
Thanks Justin for the reply.
I have through the threads about g_lie, but cannot understand how to get
the values for Elj and Eqq for a particular ligand. Like in my case for
a system consisting of a beta2AR protein + dopamine (ligand) + POPC +
water, what should be the v
Thanks Justin for the reply.
I have through the threads about g_lie, but cannot understand how to get the
values for Elj and Eqq for a particular ligand. Like in my case for a system
consisting of a beta2AR protein + dopamine (ligand) + POPC + water, what
should be the values for Elj and Eqq?
Than
Anirban Ghosh wrote:
Hi ALL,
I have run a protein + ligand (dopamine) simulation. Now I want to
calculate the free energy of binding using g_lie. But g_lie asks for two
values: Elj and Eqq. How or from where can I get these values for my
ligand? Also, do I need to run a simulation with only
Hi ALL,
I have run a protein + ligand (dopamine) simulation. Now I want to calculate
the free energy of binding using g_lie. But g_lie asks for two values: Elj
and Eqq. How or from where can I get these values for my ligand? Also, do I
need to run a simulation with only the ligand? And, is there a
Hi ALL,
I have run a protein + ligand (dopamine) simulation. Now I want to calculate
the free energy of binding using g_lie. But g_lie asks for two values: Elj
and Eqq. How or from where can I get these values for my ligand? Also, do I
need to run a simulation with only the ligand? And, is there a
Hi ALL,
I have run a protein + ligand (dopamine) simulation. Now I want to calculate
the free energy of binding using g_lie. But g_lie asks for two values: Elj
and Eqq. How or from where can I get these values for my ligand? Also, do I
need to run a simulation with only the ligand? And, is there a
vivek sharma wrote:
Hi All,
I want to use g_lie function of gromacs to calculate the binding free
energy og a ligand with the protein. For the same I need to run two MDS,
one for ligand only and one for ligand+protein complex (please correct
if I am wrong).
What are the checks that I should
Hi All,
I want to use g_lie function of gromacs to calculate the binding free energy
og a ligand with the protein. For the same I need to run two MDS, one for
ligand only and one for ligand+protein complex (please correct if I am
wrong).
What are the checks that I should take care in this case, e.
Blaise Mathias-Costa wrote:
hello all,
In my ligand enzyme simulation, I have given *energygrps: protein non
protein. *The reason is that when I gave energygrps* *give as : Protein
DRG SOL CL, the mdrun stopped at 560ps saying that the system is
physically unrealistic!
The identity of energ
hello all,In my ligand enzyme simulation, I have given energygrps: protein non protein. The reason is that when I gave energygrps give as : Protein DRG SOL CL, the mdrun stopped at 560ps saying that the system is physically unrealistic! Now I want to analyze the g_lie for the ligand, is there any
Hi MD people!
Some questions about g_lie.
My purpose is to score different ligands and get a rough estimation of
the free energy of binding between free and bound state of the ligands
and protein of interest.
1. When I run my ligands in water without the protein, should
I add counterions (Cl
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