Hi all,
I am a beginner to GROMACS and MD simulations in general. I’m trying to
model electroporation in a DPPC membrane but I am having issues with the
energy minimization step. I am basing my approach on the one followed in
Dr. Justin Lemkul’s KALP-15 in DPPC Tutorial (
On 4/28/15 8:14 AM, Abhijit Jassem wrote:
Hi all,
I am a beginner to GROMACS and MD simulations in general. I’m trying to
model electroporation in a DPPC membrane but I am having issues with the
energy minimization step. I am basing my approach on the one followed in
Dr. Justin Lemkul’s
On 2/25/15 1:15 AM, ashish bihani wrote:
Hello, I have understood my mistakes that I reported in previous queries of
this string. now, I am proceeding more systematically.
I have generated ff parameters for Inositol Pyrophosphate with the help of
PRODRG server (as mentioned in the tutorials)
Hello,
I have understood my mistakes that I reported in previous queries of this
string. now, I am proceeding more systematically.
I have generated ff parameters for Inositol Pyrophosphate with the help of
PRODRG server (as mentioned in the tutorials) as a residue and added it to
On 1/30/15 1:55 AM, ashish bihani wrote:
Hello,
I understand that .itp is a topology file. But the swissparam pack does not
have a .gro file. How do I create solvated.gro ? (which has to be used in
grompp)
Is there a way to convert .itp in .top and .gro ? GROMACS tutorial does not say
Hello all,
I have generated a PDB file for Inositol pyrophosphate using pyMOL to build the
structure from scratch. I have converted PDB to mol2 with openbabel and
submitted at Swissparam (http://swissparam.ch/) which returned a zip file
containing various files of the same name (.itp,
On 1/29/15 6:23 AM, ashish bihani wrote:
Hello all,
I have generated a PDB file for Inositol pyrophosphate using pyMOL to build the
structure from scratch. I have converted PDB to mol2 with openbabel and
submitted at Swissparam (http://swissparam.ch/) which returned a zip file
Hello,
I understand that .itp is a topology file. But the swissparam pack does not
have a .gro file. How do I create solvated.gro ? (which has to be used in
grompp)
Is there a way to convert .itp in .top and .gro ? GROMACS tutorial does not say
whether .itp can sustitute the other two.
From:
On 1/2/15 11:21 AM, Suman Das wrote:
Hi,
I am trying to simulate a mixture of Choline Chloride+Urea mixture with
33:67 ratio at 298 K. I have taken the force field of choline from this
paper :http://pubs.acs.org/doi/full/10.1021/jp404619x
January 2015 11:21
To: gmx-us...@gromacs.org
Subject: [gmx-users] Energy minimization problem in Choline Chloride+Urea
mixture in Gromacs
Hi,
I am trying to simulate a mixture of Choline Chloride+Urea mixture with
33:67 ratio at 298 K. I have taken the force field of choline from
Hi,
I am trying to simulate a mixture of Choline Chloride+Urea mixture with
33:67 ratio at 298 K. I have taken the force field of choline from this
paper :http://pubs.acs.org/doi/full/10.1021/jp404619x
Dear md,
I think I understand what you want to say. If you want the energy needed to
pull away from the binding site, try using Umbrella Sampling method. You will
get Potential of Mean Force which you are able to calculate binding constant
directly.
Best
Onur
On 11/14/14 08:52 AM, rama david
On 11/13/14 2:14 AM, md kashif wrote:
Dear all
Can anyone suggest that how to compare change in energy of my protein
before docking and after docking by a ligand.
Please suggest any suitable tutorial or paper if possible.
You can easily calculate an energy value for the protein (single
Dear md,
On docking the only change in enegy for ligand takes place. The protein is
rigid generally.
So what was your condition was it regid or flexible for some residues??
so how it can have the energy the energy of single peptide,single
protein and the energy of
docking complex is compared.
Dear all
Can anyone suggest that how to compare change in energy of my protein
before docking and after docking by a ligand.
Please suggest any suitable tutorial or paper if possible.
Thanks
--
Gromacs Users mailing list
* Please search the archive at
Dear Dr. Justin Lemkul
Thanks for your kind suggestion, I have energy minimized my protein taken
from PDB. It gives result as -1.5248922e+06. Taking the energy minimized
protein generated in .gro file file and docking it with ligand and doining
energy minimization again, it gives result as
Hi,
That value may indicate that the ligand is not horribly out of place,
because the total energy is negative. Showing a favourable binding
interaction is a different matter, for which this is just the tiniest first
step.
Mark
On Tue, Nov 11, 2014 at 9:04 AM, md kashif
On 11/10/14 2:36 AM, md kashif wrote:
Dear all
I have downloaded a protein from RCSB, having two chains. In order to go
for energy minimization should I delete one chain as both are similar and
other molecules like SO4, water etc? Is the protein having chain A only can
be used for energy
Dear all
I have downloaded a protein from RCSB, having two chains. In order to go
for energy minimization should I delete one chain as both are similar and
other molecules like SO4, water etc? Is the protein having chain A only can
be used for energy minimization using tutorial
On 11/3/14 12:57 AM, Kalyanashis Jana wrote:
Thank you very much... But I am not going to use any parent molecules like
protein or DNA. I would like to perform the gromacs simulation for this
unknown molecule.
First few lines of my topology file..
;
; File 'topol.top' was generated
; By user:
Dear all,
I am trying to run a gromacs simulation using an .itp file of an unknown
molecule ( non protein and DNA). I don't want to put the .itp file in a
forcefield folder and I would like put it in my working directory. Can you
please tell me, what is procedure to finish the energy minimization?
just put the itp file in your working directory, and include it in the
top file of your system, so that Gromacs can find it.
Hope this helps.
Victor
2014-11-02 8:54 GMT-06:00 Kalyanashis Jana kalyan.chem...@gmail.com:
Dear all,
I am trying to run a gromacs simulation using an .itp file of an
Thank you so much... I have tried to run the grompp step according to you.
But it is showing
Fatal error:
Syntax error - File A-T.itp, line 7
Last line read:
'[ atomtypes ] '
Invalid order for directive atomtypes
I have attached the .itp file and .top file.
Please kindly tell me, what to do now..
On 11/2/14 11:32 AM, Kalyanashis Jana wrote:
Thank you so much... I have tried to run the grompp step according to you.
But it is showing
Fatal error:
Syntax error - File A-T.itp, line 7
Last line read:
'[ atomtypes ]'
Invalid order for directive atomtypes
I have attached the .itp file and
Thank you very much... But I am not going to use any parent molecules like
protein or DNA. I would like to perform the gromacs simulation for this
unknown molecule.
First few lines of my topology file..
;
; File 'topol.top' was generated
; By user: kollan (506)
; On host: master.localdomain
; At
Hello All
I am trying to perform MD for protein ligand complex in popc lipid with
Charmm36 force field. I follow Justin A. Lemkul tutorial of membrane
protein simulation.
I have successfully perform till InflateGRO followed by energy minimization
step.
perl inflategro.pl em.gro 0.95 POPC 0
Thanks for your reply Justin
The error is now solve but I don't know this is a right way or not.
The step which I perform previously in which I am facing error:
Packing :
1) perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5
area_shrink1.dat
2) grompp -f em.mdp -c system_shrink1.gro
On 9/2/14, 10:49 AM, neha bharti wrote:
Thanks for your reply Justin
The error is now solve but I don't know this is a right way or not.
The step which I perform previously in which I am facing error:
Packing :
1) perl inflategro.pl em.gro 0.95 POPC 0 system_shrink1.gro 5
area_shrink1.dat
On 6/25/14, 10:12 AM, Iris Nira Smith wrote:
Hello gromacs users,
I have searched the gmx-users archive and have successfully found multiple
posts that provide advice on how to troubleshoot my issue. Unfortunately, after
trying multiple ways to troubleshoot as suggested by each of these
Hi,
Proteins do not have a single holy structure, nor is any given quantity of
MD going to find it, if it exists. Neither is there a single metric of
suitability - backbone strain as measured by Ramachandran plot deviations
could easily be the result of accommodating worse problems while stuck in
Hello
I am new user of gromacs. I am using gromacs 4.6.3
I wanted to minimize the energy of a protein. Before energy minimization the
prockeck result for Ramachandran plot was 89% in allowed region but after
energy minimization the result become worse i.e. 87%.
I was performing energy minimization
On 4/11/14, 7:47 AM, neha_bharty wrote:
Hello
I am new user of gromacs. I am using gromacs 4.6.3
I wanted to minimize the energy of a protein. Before energy minimization the
prockeck result for Ramachandran plot was 89% in allowed region but after
energy minimization the result become worse
On 11/18/13 2:36 AM, Archana Sonawani-Jagtap wrote:
Hi,
I am simulating a peptide in TFE-water system. I am getting following error:
1 particles communicated to PME node 4 are more than 2/3 times the
cut-off out o f the domain decomposition cell of their charge group in
dimension x.
This
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