By the way,
I'm also looking for a most trivial way for extraction of pdb files from my
trajectory on the desired intervals. E.g I have trajectory consisted of
5000 frames and I want to obtain 10 pdb files every each 500 frames ( or
selected time interval as the alternative ).
Commonly I do it
Dear All,
In my protein pdb file I have changed some of the amino acid residue
names. So accordingly I have changed corresponding residue names in force
filed files and kept all the files [ modified and unmodified ] in my
current working directory. Those files are
1) atomtypes.atp
2)
try ptraj
Date: Fri, 15 Jun 2012 10:18:40 +0400
Subject: Re: [gmx-users] analysing of the long trajectories
From: jmsstarli...@gmail.com
To: gmx-users@gromacs.org
By the way,
I'm also looking for a most trivial way for extraction of pdb files from my
trajectory on the desired intervals. E.g I
I've found main reason of such crushes. It was due to the individual
internal waters wich I've included to my model as the buried to the protein
interiour ( the coordinates were copppied form X-ray structure of the same
protein).
By the way I have already performed the same simulation with the
trjconv -dt
use dt flag with the utility trjconv
Chandan
--
Chandan kumar Choudhury
NCL, Pune
INDIA
On Fri, Jun 15, 2012 at 12:07 PM, a a pat...@hotmail.com wrote:
try ptraj
--
Date: Fri, 15 Jun 2012 10:18:40 +0400
Subject: Re: [gmx-users] analysing of the
Dear gmx users:
I would like to calculate chemical shift using g_chi ,but the result has
only :
*** Chemical shifts from the chemical shift index ***
PLEASE READ AND CITE THE FOLLOWING REFERENCE
D. S. Wishart and A. M. Nip
Protein Chemical Shift Analysis: A Practical Guide
HI Guys,
I'm trying to run a short equilibration of p56 tetramer in water. I issue:
/home/flores/local/gromacs/bin/mdrun -v -deffnm em -c
/home/flores/projects/antibody-design/13JUN12/352/last.2.em.pdb
The problem is that last.2.em.pdb has four chains, but none have chain ID's!
The file
On 15/06/2012 5:06 PM, Samuel Flores wrote:
HI Guys,
I'm trying to run a short equilibration of p56 tetramer in water. I issue:
/home/flores/local/gromacs/bin/mdrun -v -deffnm em -c
/home/flores/projects/antibody-design/13JUN12/352/last.2.em.pdb
The problem is that last.2.em.pdb has four
On 15/06/2012 4:27 PM, tarak karmakar wrote:
Dear All,
In my protein pdb file I have changed some of the amino acid
residue names. So accordingly I have changed corresponding residue
names in force filed files and kept all the files [ modified and
unmodified ] in my current working
hi Shay,
Can you tell me how you resolved this? I'm having the same issue.
Sam
On Nov 1, 2010, at 12:10 PM, Shay Teaching wrote:
Sorry - problem resolved :-)
On Mon, Nov 1, 2010 at 12:55 PM, Shay Teaching shay.teach...@gmail.com
wrote:
Hi everyone,
I've come across some problem: I
On 15/06/2012 3:50 PM, James Starlight wrote:
Hi Tsjerk !
I my case I want to compare large-scale dynamics with more local
events like fluctuation of the individual side chains so I suppose
that I need larger number of frames. But how exactly I could define
this number for my 100ns
On 15/06/2012 3:56 PM, delara aghaie wrote:
Dear Gromacs users
I want to compare some properties of two Interferons via MD simulation.
One comes with pdb ID : 1ITF. (It has 24 Models in single pdb file,
but each model with single chain.) I did pdb2gmx on this.
The other is with pdb ID of :
15 jun 2012 kl. 09.16 skrev Mark Abraham:
On 15/06/2012 5:06 PM, Samuel Flores wrote:
HI Guys,
I'm trying to run a short equilibration of p56 tetramer in water. I issue:
/home/flores/local/gromacs/bin/mdrun -v -deffnm em -c
Hi,
This query is related to my previous queries. I want to constraint the
psi/psi angle of the turn residue of my beta-hairpin , meaning that they
are allowed to move in certain range of psi/phi angle space.
Simultaneously, I want to freeze the movement of strand residues. This
procedure has to
On 15/06/2012 8:30 AM, Tom Dupree wrote:
Hi Mark,
Thanks for the catch on the transcription error, I think I have found it
::embarrassed::.
The repeated final value is still perplexing me. I have checked both my .xvg
from g_energy and the .edr file with gmxdump. In both cases the final step
Dear all gromacs users,
While i am running the commond trjconv
-f 1AKI_full.trr -s 1AKI_b4full.tpr -o final.pdb -dump 500 i am getting
the following warning.
WARNING no output, last frame read at t=10
Kindly tell me how to overcome this error.
Suryanarayana
Dear Users,
I've managed to obtain a well equilibrated box of 2,3 dihydroxynaphthalene
at 450K (melting point=437K) and 1 bar pressure. I've calculated hydrogen
bond distance using g_hbond and it comes to 0.267 nm. I've also calculated
the density and it comes to 1229 kg/m3 (solid density = 1120
Hi,
Thanks for the reply.
One thing, while giving the '-ff' flag it is asking for some string. So I
renamed all my force field files as except spc.itp and ions.itp. Renamed
files are .
1) ffprot.atp
2) ffprot.rtp
3) ffprot.itp [ includes ffnonbonded.itp and ffbonded.itp ]
pdb2gmx -f
Thanks.
I read that it doesn't matter if the protein moves and even protrudes the box.
It's OK, but there is a question here; why doesn't the box move rather than the
protein?
Is it possible for box to be defined every step?, then the protein would stay
in the center of the box.
On 15/06/2012 6:21 PM, tarak karmakar wrote:
Hi,
Thanks for the reply.
One thing, while giving the '-ff' flag it is asking for some string.
So I renamed all my force field files as except spc.itp and ions.itp.
Renamed files are .
1) ffprot.atp
2) ffprot.rtp
3) ffprot.itp [ includes
Thanks a lotnow it's working:)
On Fri, Jun 15, 2012 at 2:00 PM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 15/06/2012 6:21 PM, tarak karmakar wrote:
Hi,
Thanks for the reply.
One thing, while giving the '-ff' flag it is asking for some string. So I
renamed all my force
On 15/06/2012 6:27 PM, Shima Arasteh wrote:
Thanks.
I read that it doesn't matter if the protein moves and even protrudes
the box. It's OK, but there is a question here; why doesn't the box
move rather than the protein?
The box could move, but it can't accelerate, else it wouldn't be an
Hi,
All molecules diffuse. As such, proteins are expected to move about. Preventing
them form doing so is essentially non physical, so you'd need a good and
thought-through reason for doing so.
Erik
15 jun 2012 kl. 10.27 skrev Shima Arasteh:
Thanks.
I read that it doesn't matter if the
i am using the tutorial KALP15 in DPPC for my protein in bilipid
membrane SIMULATION.
i have reached Step Three: Defining the Unit Cell Adding Solvent
where i hav to pack the lipids around the protein using InflateGro.
how do i start using inflategro?
my last step was : to generate this new
On 6/15/12 4:08 AM, Seera Suryanarayana wrote:
Dear all gromacs users,
While i am running the commond trjconv -f
1AKI_full.trr -s 1AKI_b4full.tpr -o final.pdb -dump 500 i am getting the
following warning.
WARNING no output, last frame read at t=10
Kindly tell
On 6/15/12 5:58 AM, ankita oindrila wrote:
i am using the tutorial KALP15 in DPPC for my protein in bilipid
membrane SIMULATION.
i have reached Step Three: Defining the Unit Cell Adding Solvent
where i hav to pack the lipids around the protein using InflateGro.
how do i start using
On 6/14/12 5:51 PM, rainy908 wrote:
Hi,
I am currently using bootstrapping in g_wham to estimate the uncertainty in my
PMF. I use a number of 1000 bootstraps.
/software/gromacs/gromacs-4.0.7-plumed-1.2.0-x86_64/bin//g_wham \
-ip gwham.dat \
-bins 5000 \
-hist histo.xvg \
-bsres
On 6/15/12 4:08 AM, Satish Kamath wrote:
Dear Users,
I've managed to obtain a well equilibrated box of 2,3 dihydroxynaphthalene
at 450K (melting point=437K) and 1 bar pressure. I've calculated hydrogen
bond distance using g_hbond and it comes to 0.267 nm. I've also calculated
the density and
Ok, I am using v-rescale now and the major artefacts seem to be gone, at
least on the very short term (2-3 ns).
It seems grompp should warn that andersen is not a good choice if you're
using CPUs :)
Thanks!
M.
--
Massimo Sandal, Ph.D.
http://devicerandom.org
--
gmx-users mailing list
-- Forwarded message --
From: Seera Suryanarayana paluso...@gmail.com
Date: Fri, Jun 15, 2012 at 1:38 PM
Subject: Regarding error.
To: gmx-users@gromacs.org
Dear all gromacs users,
While i am running the commond trjconv
-f 1AKI_full.trr -s
On 6/15/12 6:53 AM, ms wrote:
Ok, I am using v-rescale now and the major artefacts seem to be gone, at least
on the very short term (2-3 ns).
It seems grompp should warn that andersen is not a good choice if you're using
CPUs :)
Such a warning would become outdated very soon - the 4.6
Hey,
Most statistics texts on bootstrapping will advise taking in the order
of a thousand bootstrap samples. Don't know about the number of bins,
but in any case, the problem shouldn't be that hard computationally.
Have you checked the process? Is it really still running, has it
stalled? And how
There is no box, so it can't move. There is a lattice specified by
three lattice vectors defining the periodicity. These vectors are
updated every step based on the pressure, if you use pressure
coupling. You can specify the protein to have no net center of mass
motion, by setting it as comm_grps
Dear Sir/Madam
This is Nidhi Jatana. I downloaded the lastest version of gromacs i.e.
4.5.5 from the link (ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.5.tar.gz)
and have installed it but whenever I am trying to run any of the programs,
its showing me the version to be 4.0.5. For example, I was
On 6/15/12 7:37 AM, Nidhi Jatana wrote:
Dear Sir/Madam
This is Nidhi Jatana. I downloaded the lastest version of gromacs i.e. 4.5.5
from the link (ftp://ftp.gromacs.org/pub/gromacs/gromacs-4.5.5.tar.gz) and have
installed it but whenever I am trying to run any of the programs, its showing me
Hi users,
I am seeing some unexpected behavior for my COM pulling simulations. Errors
arise from the COM and distance calculations and I reckon it can be fixed by
increasing the box size and/or choosing good atoms as pbc_atomX in the mdp
file. From the documentation it's not clear to me if
Dear Sir/Madam
I checked up in the system, there was one version of gromacs in /opt/bio/.
I removed that and I reinstalled gromacs using the following commands:
tar -xvf gromacs-4.5.5.tar.gz
cd gromacs-4.5.5
./configure --program-suffix=_mpi
make
make mdrun -j 8
make install
make
Dear All,
I am little unaware of choosing the shape and length of box while
simulating protein in water. I saw in one of the GROMACS tutorials [
http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water] in
which they have kept the protein at the center of the box and the
On 6/15/12 8:47 AM, tarak karmakar wrote:
Dear All,
I am little unaware of choosing the shape and length of box while
simulating protein in water. I saw in one of the GROMACS tutorials [
http://ringo.ams.sunysb.edu/index.php/MD_Simulation:_Protein_in_Water] in which
they have kept
On 15/06/12 13:02, Justin A. Lemkul wrote:
In the existing code for version 4.5.5, it seems the Andersen keyword
is accepted but there is no mention of its use in update.c or
coupling.c, suggesting to me that it's a ghost parameter that does
nothing. There should be some indication in the .log
On 15/06/2012 10:45 PM, Nidhi Jatana wrote:
Dear Sir/Madam
I checked up in the system, there was one version of gromacs in
/opt/bio/. I removed that and I reinstalled gromacs using the
following commands:
tar -xvf gromacs-4.5.5.tar.gz
cd gromacs-4.5.5
./configure --program-suffix=_mpi
On 6/15/12 8:45 AM, Nidhi Jatana wrote:
Dear Sir/Madam
I checked up in the system, there was one version of gromacs in /opt/bio/. I
removed that and I reinstalled gromacs using the following commands:
tar -xvf gromacs-4.5.5.tar.gz
cd gromacs-4.5.5
./configure --program-suffix=_mpi
Dear gmx users,
I am doing KALP15 in DPPC following the Justin tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
. In the second step, the first command is grompp as follow:grompp -f
minim.mdp -c dppc128.gro -p topol_dppc.top -o
On 6/15/12 10:25 AM, Shima Arasteh wrote:
Dear gmx users,
I am doing KALP15 in DPPC following the Justin tutorial
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/03_solvate.html
. In the second step, the first command is grompp as follow:
grompp -f
Thanks for your reply.
But one more question: what about when the applied lipid bilayer is POPC? Is
this .top file (topol_dppc) useful yet? How come?
You know, my main problem is that I don't know where this .top file come from?
Sincerely,
Shima
From:
On 6/15/12 10:34 AM, Shima Arasteh wrote:
Thanks for your reply.
But one more question: what about when the applied lipid bilayer is POPC? Is
this .top file (topol_dppc) useful yet? How come?
You know, my main problem is that I don't know where this .top file come from?
It was created
Thanks, got it.
Sincerely,
Shima
From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Friday, June 15, 2012 7:07 PM
Subject: Re: [gmx-users] Tutorial KALP-15 in DPPC
On 6/15/12 10:34 AM, Shima Arasteh
Nevermind. I figured it out I think. It was more of a problem with box size.
Erik
15 jun 2012 kl. 14.20 skrev Erik Marklund:
Hi users,
I am seeing some unexpected behavior for my COM pulling simulations. Errors
arise from the COM and distance calculations and I reckon it can be fixed by
On Fri, Jun 15, 2012 at 1:23 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
You can specify the protein to have no net center of mass
motion, by setting it as comm_grps in the .mdp file.
If the user is just concerned about visualization, trjconv -center
solves his problem.
--
Elton Carvalho
Thanks.
Sincerely,
Shima
From: Elton Carvalho elto...@if.usp.br
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Friday, June 15, 2012 7:43 PM
Subject: Re: [gmx-users] protein near the edges of simulation box
On Fri, Jun 15, 2012 at 1:23
Dear Elton,
Where am I supposed to use trjconv -center ? when I want to get the mdrun?
Sincerely,
Shima
From: Elton Carvalho elto...@if.usp.br
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Friday, June 15, 2012 7:43 PM
Subject: Re:
On 6/15/12 11:46 AM, Shima Arasteh wrote:
Dear Elton,
Where am I supposed to use trjconv -center ? when I want to get the mdrun?
trjconv is a post-processing command that can be used for a variety of purposes,
of which one of the more common ones is to transform coordinates for convenient
Hi,
Is there any difference between confout.gro file and last frame which we
can extract from trajectory? I am thinking they are different!!
When I see the trajectory I can see the edge of the well-shaped box, but
when I see confout.gro it is not well-shaped and some atoms looks went out
out of
On Fri, Jun 15, 2012 at 5:46 PM, Shima Arasteh
shima_arasteh2...@yahoo.com wrote:
Dear Elton,
Where am I supposed to use trjconv -center ? when I want to get the mdrun?
As Justin mentioned, you should use if after mdrun, on your .xtc
(or.trr) files. Check the manual.
--
Elton Carvalho
Tel.:
OK, but as I know the trjconv is a command after mdrun, so when I get the
output of mdrun and see it in VMD, it doesn't make different.
Now wondering what is the benefit of trjconv -center and -pbc?
Sincerely,
Shima
From: Justin A. Lemkul jalem...@vt.edu
On 6/15/12 12:19 PM, Shima Arasteh wrote:
OK, but as I know the trjconv is a command after mdrun, so when I get the
output of mdrun and see it in VMD, it doesn't make different.
Now wondering what is the benefit of trjconv -center and -pbc?
You have to load the output trajectory from
On 6/15/12 12:11 PM, Dariush Mohammadyani wrote:
Hi,
Is there any difference between confout.gro file and last frame which we can
extract from trajectory? I am thinking they are different!!
When I see the trajectory I can see the edge of the well-shaped box, but when I
see confout.gro it is
Thanks.
Sorry, what do you mean by trajectory A and B?
Sincerely,
Shima
From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Friday, June 15, 2012 9:04 PM
Subject: Re: [gmx-users] protein near the edges of
On 6/15/12 12:41 PM, Shima Arasteh wrote:
Thanks.
Sorry, what do you mean by trajectory A and B?
It's just a generic example. To be absolutely clear, let's say you have a
trajectory named md.xtc that mdrun produces. That trajectory will have
molecules that diffuse all over the place.
Oh, Thanks a lot. That is really kind of you.
Sincerely,
Shima
From: Justin A. Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Friday, June 15, 2012 9:13 PM
Subject: Re: [gmx-users] protein near the edges of
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