Inspite of having DPPC in index file,when I run the command ( i.e., grompp
-f nvt.mdp -c em.gro -p topol.top -o nvt.tpr ),I am getting the error:
Group DPPC not found in indexfile.
Maybe you have non-default goups in your .mdp file, while not using the
'-n' option of grompp.
In that case use the
Dear friends,
iam doing protein-ligand dynamics..iam getting the error like this
Group Protein_JZ4 not found in index file.
Group names must match either [moleculetype] names
or custom index group names,in which case you
must supply an index file to the '-n' option of grompp.
please help me in
On 6/02/2012 8:28 PM, Anushree Tripathi wrote:
Inspite of having DPPC in index file,when I run the command ( i.e.,
grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr ),I am getting the
error:
Group DPPC not found in indexfile.
Maybe you have non-default goups in your .mdp file, while not
On 6/02/2012 8:31 PM, RAMYA NAGA wrote:
Dear friends,
iam doing protein-ligand dynamics..iam getting the error like this
Group Protein_JZ4 not found in index file.
Group names must match either [moleculetype] names
or custom index group names,in which case you
must supply an index file to the
Dear users,
Is there any way to find out About Van Der Waals interactions between two group
of residues, by Gromacs?
regards,
sajad
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gmx-users mailing listgmx-users@gromacs.org
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Please search the archive at
where should I use -n option in the command (i.e., grompp -f nvt.mdp -c
em.gro -p topol.top -o nvt.tpr).Please tell me.
On Mon, Feb 6, 2012 at 4:58 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 6/02/2012 8:28 PM, Anushree Tripathi wrote:
Inspite of having DPPC in index file,when I run the
Anushree Tripathi wrote:
where should I use -n option in the command (i.e., grompp -f nvt.mdp -c
em.gro -p topol.top -o nvt.tpr).Please tell me.
I would suggest you refer to grompp -h and/or go through some basic tutorial
material so that you can get a feel for command line options and
James Starlight wrote:
Justin,
I've built my system in accordance to the first way from your Biphgastic
system tutorial.
I've defined system with slight biger ( on 1 nm in each dimension)
dimensions that I needed and place maximym CCl4 molecules in that box by
genbox -ci ccl4.gro -nmol
Hi
Is it possible to use amber forcefield with lipid parameters like it
was done with gmx in KALP-15 in DPPC tutorial?
I have to use amber forcefield as it is neccessary for parametrization
of my ligand and its stecking interactions.
Thank you very much
--
Nemo me impune lacessit
--
Will you please send me the basic tutorial in which I can find how to use
-n option in grompp -f nvt.mdp -c em.gro -p topol.top -o nvt.tpr command.
On Mon, Feb 6, 2012 at 5:17 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Anushree Tripathi wrote:
where should I use -n option in the command
On 6/02/2012 11:09 PM, Anushree Tripathi wrote:
Will you please send me the basic tutorial in which I can find how to
use -n option in grompp -f nvt.mdp -c em.gro -p topol.top -o
nvt.tpr command.
All the tutorials provide examples of using the general syntax
command -x value -y file.ext
Алексей Раевский wrote:
Hi
Is it possible to use amber forcefield with lipid parameters like it
was done with gmx in KALP-15 in DPPC tutorial?
I have to use amber forcefield as it is neccessary for parametrization
of my ligand and its stecking interactions.
If you can find suitable
Steven Neumann wrote:
Dear Gmx Users,
I want to create index file of my protein residues - each group
corresponds to different residue. Is there any option in make_ndx which
will allow me to do it automatically instead of typing: r 180, r 181,
... r 550?
splitres 1
That will split
Dear:
I am reading a membrane protein simulation paper by GROMACS which
published on PLOS Computational Biology (
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001053
),
titled 'Predicting Novel Binding Modes of Agonists to β Adrenergic
Receptors Using All-Atom
Thank you!!!
On Mon, Feb 6, 2012 at 1:04 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Алексей Раевский wrote:
Hi
Is it possible to use amber forcefield with lipid parameters like it
was done with gmx in KALP-15 in DPPC tutorial?
I have to use amber forcefield as it is neccessary for
/20120206/e6fab5df/attachment.html
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End of gmx-users Digest, Vol 94
Sajad Ahrari wrote:
Dear users,
Is there any way to find out About Van Der Waals interactions between
two group of residues, by Gromacs?
You can decompose various nonbonded energy contributions by using suitable
energygrps in the .mdp file. Beyond that, you'll have to be a lot more
parto haghighi wrote:
Dear gmx users
I am working on an umbrella sampling system.(lipid bilayer+drug).
I have used distance
I have used lipid as a refrence group and drug as a pull group.in
npt_umbrella mdp I have used constraint for refrence group and in
md_umbrella I have removed the
Dear Gromacs users,
I have a question related to the use of g_rdf for the calculation of
hydration of a lipid bilayer patch. I used g_rdf with -surf flag (I
tried both mol and res) and two index groups: the oxygens of waters as
first group and the atoms of the headgroups as second group. I
Steven Neumann wrote:
Dear gmx Users,
Can you please clarify me as I cannot find it anywhere what means the s0
legent in the dist.xvg as an outcome from g_dist? What is stated by |d|
? sx, sy, sz is the vector from two groups obviously.
It is the distance.
-Justin
--
Dear:
I am reading a membrane protein simulation paper by GROMACS which
published on PLOS Computational Biology (
http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1001053
),
titled 'Predicting Novel Binding Modes of Agonists to β Adrenergic
Receptors Using All-Atom
Hi all,
I have a system with a molecule called ACX plus water (molecules called SOL),
but when I try to use ACX as a group name in the .mdp file, grompp says such
a group does not exist:
---
Program grompp, VERSION 4.5.5
Source code file:
Hi Ignacio,
You can solve the problem creating an index file through make_ndx. In
such a file you need a group called ACX. Then use the index.ndx in
grompp.
Francesco
2012/2/6, Ignacio Fernández Galván jel...@yahoo.com:
Hi all,
I have a system with a molecule called ACX plus water (molecules
On 7/02/2012 2:26 AM, Qinghua Liao wrote:
Dear GMX users,
We are trying to do a simulation of a protein attached to a small
molecules, how should I do to setup the system? For the parameters of
the small molecule, I got it from ATB sever, however I don't know how
to bond the small molecule
francesco oteri wrote:
Hi Ignacio,
You can solve the problem creating an index file through make_ndx. In
such a file you need a group called ACX. Then use the index.ndx in
grompp.
In principle, an index file is not necessary here, as ACX should be generated as
a default group since it is
--- On Mon, 6/2/12, Justin A. Lemkul jalem...@vt.edu wrote:
Perhaps the OP can provide the original grompp command and
whether or not the -n flag was invoked. An incorrect
index file can also give this error, I believe, if it does
not contain the desired group.
I'm not using an index file.
It also coincides with the 1.5A RMSD change of the active site in those time
periods (see figure 2). As to the interpretation of this, maybe you should
ask the paper's authors directly? (Since they do not provide any graphs of
ligand conformation changes) And yes, I have seen chi changes like
Ignacio Fernández Galván wrote:
--- On Mon, 6/2/12, Justin A. Lemkul jalem...@vt.edu wrote:
Perhaps the OP can provide the original grompp command and
whether or not the -n flag was invoked. An incorrect
index file can also give this error, I believe, if it does
not contain the desired
Dear users,
We ve been trying unsucessfully to perform some MD simulations with
some compounds containing triple bonds using GROMACS. Does someone know
how to properly construct the topologies to this kind of bond for GROMACS ?
With my best regards,
Tanos C. C. Franca.
--
Would suggest you check to ensure that your index group and selection is for
the atoms you think it actually is, and visually inspect the system at a number
of times within the trajectory to see how the atoms are arranged relative to
each other (and measure some actual distances, easy to do
http://lists.gromacs.org/pipermail/gmx-users/2009-July/043186.html
Plus there are several others
http://www.gromacs.org/Support/Mailing_Lists/Search?q=triple+bond
Catch ya,
Dr. Dallas Warren
Medicinal Chemistry and Drug Action
Monash Institute of Pharmaceutical Sciences, Monash University
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