Hi gromacs users,
I want to perfom NVT equilibration, pull code (using pull-geometry =
direction-periodic)
Prior to this step, energy minimization (500 steps) and NPT equilibration
(5 steps) was done
As I am new to gromacs and simulations, can anyone tell me whether the
following NVT c
Hi gromacs users,
I want to calculate delta G for protein ligand binding.
Had run the umbrella pulling simulation for 100 ps (protein ligand solvated
in water), applying restraint in the protein (using the code in gromacs
tutorial website, Bevenlab).
But, after running the perl script (p
Did you try PRODRG server?
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of RAHUL SURESH
Sent: Thursday, March 2, 2017 9:53 AM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] topology
Dear Justin
Is there anything I can do to make thi
Hi gromacs users,
How to split residue 2?
Here, there are two identical organic compounds in water.
Each compound has 29 atoms (consisting of carbon, nitrogen and hydrogen)
Gave the command splitres 2.
How to proceed after that?
0 System : 9664 atoms
1 Other :
that comes from cygwin.
Be sure you read things like
https://cygwin.com/cygwin-ug-net/using-effectively.html so you understand
your own tools.
Mark
On Tue, Feb 28, 2017 at 11:54 AM Subashini .K
wrote:
> Hi,
>
>
> Thank you for the reply.
>
>
> WINDOW represents the distance
on behalf of Mark Abraham
Sent: Tuesday, February 28, 2017 2:31 PM
To: gmx-us...@gromacs.org
Subject: Re: [gmx-users] ERROR IN BASH SCRIPTING
Hi,
Looks like you edited on Windows last. Use dos2unix now, or a proper text
editor next time ;-)
Mark
On Tue, 28 Feb 2017 08:14 Subashini .K wrote
Hi gromacs users,
I use the following run.sh in the working directory of simulations
#!/bin/bash
set -e
for ((i=0;i<27;i++)); do
x=$(echo "0.05*$(($i+1))" | bc);
sed 's/WINDOW/'$x'/g' mdp/min.mdp > grompp.mdp
gmx grompp -o min.$i -pp min.$i -po min.$i -n index.ndx
gmx mdrun -
Hi gromacs users,
I want to use oplsaa force field for my organic compound.
Can anyone tell me how to install topolbuild 1.3 and thereby generate .GRO,
.ITP and .TOP with opls-aa parameter incorporated in it?
Thanks,
Subashini.K
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Many tutorials suggest to run two equilibrations and then production file.
At first, run a restrained equilibrium.
Then non-restrained equilibrium followed by production file.
Do not know the aim of your simulations.
Hope this answer helps.
Thanks,
Subashini.K
__
Hi gromacs users,
I want to calculate the binding energy (ΔGbind) using umbrella sampling method
(between protein and ligand which is solvated in water)
How to custom index groups for the pulling simulation?
The protein under consideration has only one chain A.
Thanks,
Subashini.K
--
G
Hi gromacs users,
In order to calculate binding energy of single protein inhibitor complex
through simulations, how long should we run the calculations?
Is 2ns sufficient?
How to obtain results and plot time (in ps) along x-axis and binding energy
(kJ/mol)along y-axis?
Had completed two e
rding to the default search
cutoff. The first column is your simulated time in ps.
Alex
On 2/11/2017 1:00 AM, Subashini .K wrote:
> Hi gromacs users,
>
>
> After protein ligand simulations, gave the following command to detect
> hydrogen bond
>
>
> gmx hbond -f npt.trr
Hi gromacs users,
After protein ligand simulations, gave the following command to detect hydrogen
bond
gmx hbond -f npt.trr -s npt.tpr -num hbond.xvg
After selecting protein and ligand
Obtained the following result
I am a beginner. Could someone help me to interpret these numbers? The
s
Hi gromacs users,
Have completed protein ligand simulations for 2 ns.
How to view the position fluctuations of the ligand inside the protein and
observe stable binding modes?
How to extract useful information post simulations?
Thanks,
Subashini.K
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* Please
__
From: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Subashini .K
Sent: 08 February 2017 00:08:57
To: gmx-us...@gromacs.org
Subject: [gmx-users] Radial distribution function for larger distances
Hi Gromacs users,
How to calculate RDF for larger distances, say 15 angstrom usin
Hi Gromacs users,
How to calculate RDF for larger distances, say 15 angstrom using the following
code. In which line should we focus to make changes?
Can someone help?
integrator = md
dt = 0.002 ; 2 fs
nsteps = 500 ; 10.0 ns
ns
markl...@kemi.uu.se<mailto:erik.markl...@kemi.uu.se>
On 6 Feb 2017, at 13:06, Subashini .K
mailto:subashi...@hotmail.com>> wrote:
Hi gromacs users,
I want to visualize the results of simulations using the command
gmx trjconv -s em.gro -f eq.xtc -e 1000.0 -o movie.pdb
Wish to see P
Hi gromacs users,
I want to visualize the results of simulations using the command
gmx trjconv -s em.gro -f eq.xtc -e 1000.0 -o movie.pdb
Wish to see Protein and ligand simulations together in the pdb file.
But, when the command is given, we can either select protein group or ligand
group
Hi Gromacs users,
I am new to simulation dynamics.
On what basis do we add water molecules to the protein ligand complex?
Should we ensure that the system is fully solvated?
Or, can we consider simulation without solvent (water molecules)?
Thanks,
Subashini.K
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Gromacs Users mailin
Hi gromacs users,
Through NVT equilibration, had obtained nvt.gro and nvt.trr.
Are these files sufficient to visualize protein folding?
What option in VMD has to be explored to observe protein folding?
Thanks,
Subashini.K
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http
Hi gromacs users,
What are the steps for simulation to observe protein folding in gromacs?
Thanks,
Subashini.K
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[gmx-users] REGARDING TOPOLOGY FILE
can you please recognize that two extra atoms generated by acepype??
On Jan 19, 2017 4:00 PM, "Subashini .K" wrote:
> Thank you very much for the reply.
>
>
> Actually, tried converting the ligand alone to .top and .gro file.
>
&g
atoms
should be in parallel with all the atoms existed in the gro file
this way you may solve the problem
good luck
On Jan 19, 2017 3:20 PM, "Subashini .K" wrote:
> Hi,
>
>
>
> Thank you for the reply. As I said earlier, there is one ligand molecule
> surrounded
atoms in topology file and gro file does
not match
In last line of topology file define the ligand molecule.
here is the exapmle
[ molecules ]
; Compound#mols
Protein_chain_A 1
DRG 1
On Thu, Jan 19, 2017 at 10:55 AM, Subashini .K
wrote:
> Hi gromacs users,
>
&
Hi gromacs users,
Had taken one organic molecule (ligand) and many water molecules using tleap of
Amber tools 15.
Then generated .top and .gro file using acpype by the command,
acpype -p com_solvated.top -x com_solvated.crd -b ligand
However, while using the same for gromacs, obtained the f
Hi gromacs users,
While preparing the .rtp file, what does the third and fourth column describe?
; Methane
[ CH4 ]
[ atoms ]
C opls_138-0.240 1
H1 opls_140 0.060 1
H2 opls_140 0.060 1
H3 opls_140 0.060 1
H4 opls_140 0.060 1
Doe
Hi,
I am learning to prepare the residue topology file (.rtp file) .
While preparing the file, what does the third and fourth column describe?
This is the example of methane. What do the numbers -0.240 and 1 convey?
Similarly 0.060 and 1?
[ bondedtypes ]
; bonds angles dihedrals improper
: gromacs.org_gmx-users-boun...@maillist.sys.kth.se
on behalf of Subashini .K
Sent: Saturday, January 14, 2017 12:04:40 PM
To: gmx-us...@gromacs.org
Subject: [gmx-users] converting pdb file to gromacs input file
Hi gromacs users,
I am a new gromacs user.
I wanted to generate a .gro, .itp, .conf file
Hi gromacs users,
I am a new gromacs user.
I wanted to generate a .gro, .itp, .conf file using the command
$ gmx pdb2gmx -f lig.pdb
However, the pdb file must be in the required format.
What should we type instead of LIG corresponding to each and every atom?
This is an example file of ph
Hi gromacs users,
I am using gromacs in windows 7, 64 bit.
When the following command was given,
gmx g_energy -f ener.part0001.edr -o vol.xvg
the error was
GROMACS: gmx, VERSION 5.1.1
Executable: /usr/local/gromacs/bin/gmx.exe
Data prefix: /usr/local/gromacs
Command line:
gmx
Hi gromacs users,
I am working on protein-ligand simulation..The commands were given in the
following order
(1)
source leaprc.ff14SB
loadAmberParams frcmod.tip4pew
loadAmberParams frcmod.ionsjc_tip4pew
source leaprc.gaff
LIG = loadmol2 LIG.mol2
loadamberparams LIG.frcmod
check LIG
receptor =
Hi gromacs users,
I got an error when the following command
gmx grompp -f em.mdp -c complex_GMX.gro -p complex_GMX.top -o em
The corresponding em.mdp was
; to test
; grompp -f em.mdp -c test_GMX.gro -p test_GMX.top -o em.tpr -v
; mdrun -v -deffnm em
#Grompp minimization
integrator = steep
ces, Beijing, China
At 2017-01-11 16:24:16, "Subashini .K" wrote:
>Hi,
>
>
>I have installed gromacs in cgywin.
>
>I want to run these commands
>
>
>#em.mdp
>; to test
>; grompp -f em.mdp -c test_GMX.gro -p test_GMX.top -o em.tpr -v
>; mdrun -v -de
Hi,
I have installed gromacs in cgywin.
I want to run these commands
#em.mdp
; to test
; grompp -f em.mdp -c test_GMX.gro -p test_GMX.top -o em.tpr -v
; mdrun -v -deffnm em
I had sourced gmrx before typing these commands.
source /usr/local/gromacs/bin/GMXRC
But, it says, -bash: syntax e
th.se
Subject: Re: [gmx-users] ENERGY MINIMIZATION
Hi,
In a cygwin terminal, having source'd GMXRC (see the install guide), just
like you need to do under Linux.
Mark
On Tue, Jan 10, 2017 at 7:29 PM Subashini .K wrote:
> Hi Gromacs users,
>
>
> I have installed gromacs in w
Hi Gromacs users,
I have installed gromacs in windows 7, 64 bit using cgywin.
I want to use the em.mdp file to grompp and generate a .tpr file.
In which terminal should the following commands be executed?
; to test
; grompp -f em.mdp -c test_GMX.gro -p test_GMX.top -o em.tpr -v
; mdrun -v -
Hi Gromacs users,
While using the tleap of AmberTools 15,
we give the following command
source /home/admin/amber14/dat/leap/cmd/leaprc.ff14SB
However, the following error is shown in cgywin command prompt
-bash: logFile: command not found
-bash: addAtomTypes: command not found
-bash:
Hi Gromacs users,
I am new to Gromacs. Have installed it in windows 7.
Had followed the instructions this website
https://winmostar.com/en/gmx4wm_en_win.html
How to run a test file through cygwin? Can someone help?
Thanks,
Subashini.K
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