Dear all,I am using umbrella sampling tutorial (Justin tutorial). I just
wondering the binding energy is Gibbs free energy or Helmholtz free energy?and
how can I find the difference between these two free energies?
Thanks,Negar
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Dear all,
I used Justin's tutorial(Tutorial 3: Umbrella Sampling: GROMACS Tutorial ) for
my file which is protein-ligand complex.
The pulling force was in Y direction. when Umbrella sampling finished, "Wham"
couldn't analysis the data because wham is in z direction.what should I do now
for wham
Dear all,
I used Justin tutorial(Tutorial 3: Umbrella Sampling: GROMACS Tutorial ) for my
file which is protein-ligand complex.
The pulling force was in Y direction. when Umbrella sampling finished, "Wham"
couldn't analysis the data because wham is in z direction.what should I do now
for wham a
Dear all,I used Justin's tutorial(Tutorial 3: Umbrella Sampling: GROMACS
Tutorial ) for my file which is protein-ligand complex.
The pulling force was in Y direction. when Umbrella sampling finished, "Wham"
couldn't analysis the data because wham is in z direction.what should I do now
for wham
Dear all, I used Justin's tutorial(Tutorial 3: Umbrella Sampling: GROMACS
Tutorial ) for my file which is protein-ligand complex.
The pulling force was in Y direction. when Umbrella sampling finished, "Wham"
couldn't analysis the data because wham is in z direction.what should I do now
for wham
Dear all,
I have a protein_Ligand complex which I want do Umbrella Sampling on it to
find out free energy.for this purpose I used Justin tutorial(Tutorial 3:
Umbrella Sampling: GROMACS Tutorial ).
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GROMACS Tutorial
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Here is my questiones:in tutorial he said:
Acetyl
Dear all,
I have a protein_Ligand complex which I want do Umbrella Sampling on it to
find out free energy.for this purpose I used Justin tutorial(Tutorial 3:
Umbrella Sampling: GROMACS Tutorial ).
|
|
|
GROMACS Tutorial
|
|
|
Here is my questiones:in tutorial he said:
Acetyla
Dear all,
I have a protein_Ligand complex which I want do Umbrella Sampling on it to
find out free energy.for this purpose I used Justin tutorial(Tutorial 3:
Umbrella Sampling: GROMACS Tutorial ).
|
| |
GROMACS Tutorial
| |
|
Here is my questiones:in tutorial he said:
Acetyla
Dear all users,
I am using tutorial Kalp15 in DPPC from Justin's tutorials.I want to remove
waters which are between bilayers so I use this script:
http://www.gromacs.org/Documentation/How-tos/Membrane_Simulations
#!/bin/bash
# give x.gro as first command line arguement
upperz=6.417
lowerz=0.820
Dear all Gromacs users, I want to simulate prolactin receptor in a mixed
DPPC-DMPC bilayer. At first, I will insert the trans membrane part of the
protein (prolactin receptor) in the bilayer and do the necessary modifications
to the FF, according to the Justin,s membrane protein tutorial.
It sho
Dear all Gromacs usersI have started the tutorial on membrane protein, provided
by Justin ( KALP 15 in model membrane).Now I have two questions:1) Why Justin
adds the ACE and NH2 groups to the two ends of the peptide model?
The -ter option in pdb2 gmx command can add interactively the NH2 or NH3+
Dear all users,
I am new to Gromacs and I want to simulate a box of pure water.I want to know
is there any tutorial for this simulation with Gromacs? or Could anyone kindly
help me?
Thanks in advance,Negar
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Dear all users,
I have a question about characters.I want to simulate protein-ligand complex
from Justin Lmkul tutorial .When I run this line:gmx editconf -f complex.gro -o
newbox.gro -bt dodecahedron -d 1.0I get this error:"Fatal error:An input file
contains a line longer than 4096 characters w
Dear all users,
I want to install gromacs on my PC, but I don't know which operating system is
better: linux or windows and it is important that doesn't loose capabilities of
the software? In any case, which version of operating system is better for
installation?
Thanks in advance,Negar
--
Grom
Dear all users,
I am new in membrane proteins simulation. I want to simulate a membrane protein
that it is a part of a large protein and has a big extracellular part.Here is
my question: is it ok, I just simulate the membrane part even it is a part of a
large protein? and if the answer is yes
Hello friends,
I want to dock a simulated protein like: human serum albumin to the drug. I was
wondering if i could use docking with gromacs or other softwares?If I can use
gromacs docking, where can i find a good tutorial ?
thank you,Negar.Parvizi
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Dear Gromacs users
we want to simulate 1EA1 pdf file using gromacs. (according to justin tutorial).
This pdf file contains two cofactors including TPF and HEM. Our next step is to
dock some antifungal drugs to this protein which is cytochrome of the fungi.
As the TPF was not located in the act
Dear Gromacs users
we want to simulate 1EA1 pdf file using gromacs. (according to justin tutorial).
This pdf file contains two cofactors including TPF and HEM. Our next step is to
dock some antifungal drugs to this protein which is cytochrome of the fungi.
As the TPF was not located in the act
Dear Gromacs users
I have submitted a simulation for 10 ns. Now when I started to plot the graphs
such as RMSD, I saw that it has stopped at 8 ns. The point is that although the
run has stopped before specified time, I see in md.log file the time report for
the simulation, the same as report tha
Dear Gromacs users
I have submitted a simulation for 10 ns. Now when I started to plot the graphs
such as RMSD, I saw that it has stopped at 8 ns. The point is that although the
run has stopped before specified time, I see in md.log file the time report for
the simulation, the same as report tha
Dear Gromacs users
I have submitted a simulation for 10 ns. Now when I started to plot the graphs
such as RMSD, I saw that it has stopped at 8 ns. The point is that although the
run has stopped before specified time, I see in md.log file the time report for
the simulation, the same as report tha
Dear Gromacs users
I have submitted a simulation for 10 ns. Now when I started to plot the graphs
such as RMSD, I saw that it has stopped at 8 ns. The point is that although the
run has stopped before specified time, I see in md.log file the time report for
the simulation, the same as report tha
Dear Gromacs users;
I use Gromacs version 4.5.4. I finished protein-ligand complex
tutorial(Dr.justin lemkul tutorial). Now i want to use my ligand. I am new in
this field(charge group blocking). For getting an idea about charge group
blocking, i check .rtp files.
cheking aminoacides.rtp files
Dear Gromacs Users,
Does anyone know where i can get 'GROMOS96 manual and user guide'(van
Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hünenberger, P. H.; Krüger,
P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. Biomolecular Simulation: The
GROMOS96 Manual and User Guide; vdf Hochschulverlag
would be greatly appreciated.
N.P
On Sunday, June 8, 2014 11:41 PM, Justin Lemkul wrote:
On 6/8/14, 2:34 PM, Negar Parvizi wrote:
> Dear Gromacs Users,
>
> Does anyone know, where can i find information about "Gromos96 building
> blocks for suitable chargegroupings"
On Sunday, June 8, 2014 11:04 PM, Negar Parvizi wrote:
Dear Gromacs Users,
Does anyone know, where i can find information about "Gromos96 building blocks
for suitable chargegroupings"?
Thanks in advance,
N.P
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Dear Gromacs Users,
Does anyone know, where can i find information about "Gromos96 building blocks
for suitable chargegroupings"?
Thanks in advance,
N.P
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than 200 mutants and only the wt pdb was available.
cheers,
Fra
On 3 June 2014 13:19, Negar Parvizi wrote:
Dear Gromacs users
>>
>>I have a question about protein simulation in Gromacs. We are interested in
>>the effect of single point mutation on the structure of HSA
Dear Gromacs users
>
>I have a question about protein simulation in Gromacs. We are interested in
>the effect of single point mutation on the structure of HSA (human serum
>albumin) protein.
>
>We selected a pdb file for wild type HSA and submitted it for MD simulation.
>One of the mutatns of HSA
Dear all users,
I am using Protein-Ligand Complex tutorial (Justin Lemkul tutorial). For making
.pdb file of ligand, we should use PRODRG(draw molecule with JME Editor).
Here is my question that when i draw my ligand in JME Editor, which conformer
should i select ? because different conformer g
Dear Users ;
Does anyone has program "that is, the program is doing fixes" for repairing
missing residues in Swiss pdb viewer ?
Would you please send it for me?
Regards
N.Parvizi
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