On 6/6/17 2:34 AM, Apramita Chand wrote:
Dear Andre,
I added around 56 molecules of urea to 966 water. The peptide is just 6
residues and I just wanted to see its preferred conformations as well as
hydrogen bonding.
I will definitely try to extend the simulation to atleast 100ns.
For the equili
On 6/6/17 2:16 AM, Debraj Das wrote:
Dear Justin,
I am getting error with
gmx_mpi densorder -s topol.tpr -f traj.trr -n index.ndx -o density.dat
It will not write anything in that file.
If you want help solving this, you have to tell us exactly what the error was.
I have also tried gmx den
On 6/6/17 2:12 AM, RAHUL SURESH wrote:
Dear Users
*Exp procedure:*
I have simulated the protein monomer for 150ns. Using the 150ns conformer,
ligand is docked to the protein using autodock and the simulation is
carried out for 50ns.
*Analysis:*
Is it possible to compare my RMSD, RMSF, ROG an
Hi all GMX usersI want to do MD simulation on protein-ligand complex. There are
two calcium ions in the protein structure. These ions play an important role.
In the equilibration step, should I consider protein,ligand and calcium ions
as one single entity (for tc_grps option)? or should I consi
Hi All,
I have used below mdp options in GROMACS version 5.0.4. ; minim.mdp - used as
input into grompp to generate em.tpr
integrator = steep ; Algorithm (steep = steepest descent
minimization)
emtol = 1000.0; Stop minimization when the maximum force <
1000.0 kJ/mo
Hi!
I'm not sure Verlet was already implemented in GMX 4.5.5, but check the
manual for that version (or the closest one).
Cheers,
/J
On Tue, Jun 6, 2017 at 3:27 PM, wrote:
> Hi All,
> I have used below mdp options in GROMACS version 5.0.4. ; minim.mdp - used
> as input into grompp to generate
Yeah, I just checked and GMX < 4.6 does not come with Verlet (the list I
mean, not the integration).
/J
On Tue, Jun 6, 2017 at 5:45 PM, João Henriques wrote:
> Hi!
>
> I'm not sure Verlet was already implemented in GMX 4.5.5, but check the
> manual for that version (or the closest one).
>
> Che
Dear Justin
Thank you. I am considering Rmsd rmsf rg as just supplementary analysis
for my study. My aim to analyse conformational change in protein. I would
like to bring a note on protein stability after ligand binding. I don't
know to which part of monomer I can compare the rmsd of complex w
Hi João,
Thank you very much. I removed this line from the mdp file.
Regards,Mohammad
From: João Henriques
To: gmx-us...@gromacs.org; mohammad.r0...@yahoo.com
Sent: Tuesday, 6 June 2017, 20:18:51
Subject: Re: [gmx-users] mdp options in GROMACS 4.5.5
Yeah, I just checked and GMX <
Hi all,
I have used the steepest descent method to minimise my system. It kept saying
certain water molecules could not be settled but it still managed to reached
the maximum force. Then I used the Conjugate gradient method and I get this
error message. Can someday please tell me how I would ch
Dear GROMACS users, I want to estimate binding free energy for small ligand
using procedure from article doi:10.1021/jp0217839 that imlies application of
one distance, two angle and three dihedral restraints to ligand relatively to
receptor. These restraints are controlled by option
restraint-
On 6/6/17 8:22 AM, Mahboobeh Eslami wrote:
Hi all GMX usersI want to do MD simulation on protein-ligand complex. There are
two calcium ions in the protein structure. These ions play an important role.
In the equilibration step, should I consider protein,ligand and calcium ions
as one single
On 6/6/17 3:45 PM, Геннадий Макаров wrote:
Dear GROMACS users, I want to estimate binding free energy for small ligand
using procedure from article doi:10.1021/jp0217839 that imlies application of
one distance, two angle and three dihedral restraints to ligand relatively to
receptor. These r
On 6/6/17 1:11 PM, RAHUL SURESH wrote:
Dear Justin
Thank you. I am considering Rmsd rmsf rg as just supplementary analysis
for my study. My aim to analyse conformational change in protein. I would
like to bring a note on protein stability after ligand binding. I don't
know to which part of
Dear Justin
I think I have confused so much.
Let me try to put it in simple way.
1.Can I compare Rmsd , rg , rmsf of protein-ligand complex with that of
monomer(just protein) to explain stability?
2. Time step of monomer(just protein) simulation is 150ns and
protein-ligand complex is 50ns. In th
Dear all,
I want to calculate the relaxation of pure water cell at room temperature
and at freezing point, monitoring its equilibration in volume and in
potential energy. I have 3 question: 1) Can I use packmol for my initial
configuration? if there is any other option,please tell me. 2) Can I use
Dear Users
When I try to execute ramachandran plot analysis, I get the following note
like "Dihedral around 5809,5816 not found in topology. Using mult=3"
(nearly 30-40 dihedrals). What is it about?
Input is just protein structure extended upto 150ns.
--
*Regards,*
*Rahul Suresh*
*Research Scho
Hi,
Initially, my topology file can run grompp with .mdp and .gro. However,
after putting POSRES in my mdp, the warning "number of coordinates does not
match" and there is no coordinate recognized in my topology file anymore.
Therefore, the option POSRES somehow changes everything.
The topology f
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