On 2012-01-06 05:40:24PM +, Anna Duncan wrote:
In my analysis, I want to look at the minimum distance between each
lipid 'atom' and the protein and, for each timepoint, record the
residue or 'atom' in the protein that the lipid 'atom' is closest to.
I can find the minimum distance
Hello,
I'm really sorry, please ignore my last post. I realised after I
posted it that my British way of spelling 'centre' might have been
preventing me from finding many previous posts on the topic. Indeed,
when I searched a bit it became apparent to me that all I need to do
is use
Hi,
I embedded my protein of interest into a DMPC membrane by the g_membed tool
with the following command:
g membed -f input.tpr -p system.top -n index.ndx -xyinit 0.1 -xyend 1.0 -nxy
1000 -zinit 1.1 -zend 1.0 -nz 100
I then energy minimized the resultant structure for 1 ns before the
On 19/09/2011 9:42 AM, Sweta Iyer wrote:
Hi,
I embedded my protein of interest into a DMPC membrane by the g_membed
tool with the following command:
g membed -f input.tpr -p system.top -n index.ndx -xyinit 0.1 -xyend
1.0 -nxy 1000 -zinit 1.1 -zend 1.0 -nz 100
I then energy minimized the
Unfortunately genbox will put waters anywhere there is a space, including
inside the membrane. This can easily be fixed by making a script to remove
waters that are z +/- ~2 nm from the membrane center (you should run
g_density on the system to figure out the optimal distance filter). You can
Michael Daily wrote:
Unfortunately genbox will put waters anywhere there is a space,
including inside the membrane. This can easily be fixed by making a
script to remove waters that are z +/- ~2 nm from the membrane center
(you should run g_density on the system to figure out the optimal
Also it is possible that there might be a problem with setting up the
membrane. Have you tried running the membrane without protein?
-Shay
On Sep 19, 2011 3:32 AM, Justin A. Lemkul jalem...@vt.edu wrote:
Michael Daily wrote:
Unfortunately genbox will put waters anywhere there is a space,
Dear All
in membrane protein tutorial:
What is the P-N vector?
RMSD for what group do I need to calculate?
How can I estimate the helix tilt?
Thanks in advance
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Please search the archive at
Dear All
doing membrane protein tutorial of Dr.Justin I have a few question,
1-Why do I need to know the stabilization state of my box vector?
2-How can I do this (with wich program?)?
3-What can I do if they were not stable?
Thanks in advance
Mohsen
--
gmx-users mailing list
-users-boun...@gromacs.org] On Behalf Of mohsen ramezanpour
Sent: Wednesday, 9 March 2011 7:01 AM
To: Discussion list for GROMACS users
Subject: [gmx-users] Membrane Protein Tutorial
Dear All
doing membrane protein tutorial of Dr.Justin I have a few question,
Please let me know their answers.
1
Dear all
I am doing Membrane -protein tutorial.
Actually I did each step carefully,I could score down my lipids 26 times.
But there were two problems:
1-I get ~77 A for area per lipid in 26th step not 71 as Dr.Justin has said
2-I tried to do more iteration to make closer my area per lipid to
mohsen ramezanpour wrote:
Dear all
I am doing Membrane -protein tutorial.
Actually I did each step carefully,I could score down my lipids 26 times.
But there were two problems:
1-I get ~77 A for area per lipid in 26th step not 71 as Dr.Justin has said
2-I tried to do more iteration to make
Dear Dr.Justin
Yes,I know,it deleted some lipids according to inflateGRO script in the
first timethat I used perl command.
Besides:
I did iteration 25 times correctly,and no addition or doubling was occured.
I used the same commands of 25th iteration.of course I changed numberes
from 25 to 26 in
mohsen ramezanpour wrote:
Dear Dr.Justin
Yes,I know,it deleted some lipids according to inflateGRO script in the
first timethat I used perl command.
Besides:
I did iteration 25 times correctly,and no addition or doubling was occured.
I used the same commands of 25th iteration.of course I
Dear Dr.justin
Thank you.You are right.
I did what you said.
please let me know the answer of my other question in first email:
I am doing iteration more than 26 times that you said in your tutorial.
I am in 28th step now and my area per lipid is 63 and I think it is lowering
everytimes I do
mohsen ramezanpour wrote:
Dear Dr.justin
Thank you.You are right.
I did what you said.
please let me know the answer of my other question in first email:
I am doing iteration more than 26 times that you said in your tutorial.
I am in 28th step now and my area per lipid is 63 and I think it is
Ok.Thank you very much
On Mon, Mar 7, 2011 at 6:29 PM, Justin A. Lemkul jalem...@vt.edu wrote:
mohsen ramezanpour wrote:
Dear Dr.justin
Thank you.You are right.
I did what you said.
please let me know the answer of my other question in first email:
I am doing iteration more than 26
Dear Dr.Justin
Is there any criteria for choosing vdwradii for carbon atoms?
Because I have changed it from 0.15 to 0.375,but there were afew water
molecules,it is difficult to delete them manually.
then I decided to increase the vdwradii to 0.450
it is better now but i think the gap between
mohsen ramezanpour wrote:
Dear Dr.Justin
Is there any criteria for choosing vdwradii for carbon atoms?
Because I have changed it from 0.15 to 0.375,but there were afew water
molecules,it is difficult to delete them manually.
then I decided to increase the vdwradii to 0.450
it is better now
Hi,
I have done MD simulations of membrane-protein. I want to calculate interaction
energies between protein and headgroup, protein and hydrophobic core (in the
bilayer).
Please can anyone suggest me the method that should be followed to carry out
these analysis.
kind regards and best
Poojari, Chetan wrote:
Hi,
I have done MD simulations of membrane-protein. I want to calculate
interaction energies between protein and headgroup, protein and hydrophobic
core (in the bilayer). Please can anyone suggest me the method that should be
followed to carry out these analysis.
Dear all,
I am busy following the EMBO tutorial on membrane proteins
(http://www.dddc.ac.cn/embo04/practicals/9_16.htm) but it is 2 days
now that the server is down. Does anybody maybe know another url where
I can find this tutorial?
Thanks!
Irene
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gmx-users mailing list
hi i'm new to gromacs and want to simulate a protein inside a phospholipid
envelop (may be box or dodecahedron). for this i got the pdb files of both the
proteins and the lipids(e.g.POPC, POPE etc). but i'm facing a lot of problems
in generating the topology files as well as in running grompp
Samik Bhattacharya wrote:
hi i'm new to gromacs and want to simulate a protein inside a
phospholipid envelop (may be box or dodecahedron). for this i got the
pdb files of both the proteins and the lipids(e.g.POPC, POPE etc). but
i'm facing a lot of problems in generating the topology files
Thanx Justin...i must go throuh that tutorial. thanx for the help.
--- On Fri, 29/5/09, Justin A. Lemkul jalem...@vt.edu wrote:
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] membrane protein simulation
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Friday
...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org
mailto:gmx-users-boun...@gromacs.org] *On Behalf Of *Pawan Kumar
*Sent:* Thursday, 9 April 2009 2:39 PM
*To:* jalem...@vt.edu mailto:jalem...@vt.edu; Discussion list
for GROMACS users
*Subject:* Re: [gmx-users
*Subject:* Re: [gmx-users] Membrane protein tutorial
Hello sir,
Thanks for such a explanatory tutorial.
I am stuck with one error now.
I have protein, popc, sol and cl- in my system.
I have merged the sol and cl- using make_ndx.
But when I
...@vt.edu mailto:jalem...@vt.edu; Discussion list
for GROMACS users
*Subject:* Re: [gmx-users] Membrane protein tutorial
Hello sir,
Thanks for such a explanatory tutorial.
I am stuck with one error now.
I have protein, popc, sol and cl- in my system
:* Thursday, 9 April 2009 2:39 PM
*To:* jalem...@vt.edu mailto:jalem...@vt.edu; Discussion list
for GROMACS users
*Subject:* Re: [gmx-users] Membrane protein tutorial
Hello sir,
Thanks for such a explanatory tutorial.
I am stuck with one error now
Hi Justin,
Pretty neat. Thnx! Just a few comments, also on the lysozyme one. I
think it's best to name and explain all options you use for a program,
to take as much of the 'magic' out as possible. Having unexplained
options may make students, mainly undergrads, go into a non-absorbant
mode, just
problem begins to resemble
a nail.
--
Message: 2
Date: Tue, 07 Apr 2009 19:55:28 -0400
From: Justin A. Lemkul jalem...@vt.edu
Subject: [gmx-users] Membrane protein tutorial
To: Gromacs Users' List gmx-users@gromacs.org
Message-ID: 49dbe7f0.4040...@vt.edu
Content-Type
Hi Tsjerk,
Thanks for the comments. I'll think about adding some tips and tricks related
to other box types; it may be useful when new users ask, why does my system
look so funny? The lysozyme tutorial was intended to be a teaching tool for
us, anyway, as we are developing a new course
Hi Justin,
A handout may be as simple as an all-in-one html page :)
I think that especially for teaching you want to use a rhombic
dodecahedron to 1. teach good habits and 2. explain PBC (jumping
molecules).
Cheers,
Tsjerk
On Wed, Apr 8, 2009 at 12:59 PM, Justin A. Lemkul jalem...@vt.edu
Tsjerk Wassenaar wrote:
Hi Justin,
A handout may be as simple as an all-in-one html page :)
I think that especially for teaching you want to use a rhombic
dodecahedron to 1. teach good habits and 2. explain PBC (jumping
molecules).
Indeed, a single page is quite simple, here you go:
Hello sir,
Thanks for such a explanatory tutorial.
I am stuck with one error now.
I have protein, popc, sol and cl- in my system.
I have merged the sol and cl- using make_ndx.
But when I run grompp I get the error like this popc not defined in the
index file.
The grompp command : grompp -f pr.mdp
Pawan Kumar wrote:
Hello sir,
Thanks for such a explanatory tutorial.
I am stuck with one error now.
I have protein, popc, sol and cl- in my system.
I have merged the sol and cl- using make_ndx.
But when I run grompp I get the error like this popc not defined in the
index file.
The grompp
-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of Pawan Kumar
Sent: Thursday, 9 April 2009 2:39 PM
To: jalem...@vt.edu; Discussion list for GROMACS users
Subject: Re: [gmx-users] Membrane protein tutorial
Hello sir
Hello Mark Sir,
I have tried that way also.
The command i used was grompp -f pr.mdp -n index.ndx -c box_em.pdb -p
topol.top -o box_pr.tpr
But this time i get an error like this Atom 1 defined in multiple groups (1
3).
How to overcome this error ?
Thanking you,
Pawan
On Thu, Apr 9, 2009 at
*Subject:* Re: [gmx-users] Membrane protein tutorial
Hello sir,
Thanks for such a explanatory tutorial.
I am stuck with one error now.
I have protein, popc, sol and cl- in my system.
I have merged the sol and cl- using make_ndx.
But when I run grompp I get the error like this popc
Pawan Kumar wrote:
Hello Mark Sir,
I have tried that way also.
The command i used was grompp -f pr.mdp -n index.ndx -c box_em.pdb -p
topol.top -o box_pr.tpr
But this time i get an error like this Atom 1 defined in multiple
groups (1 3).
How to overcome this error ?
You can't have the
Hello sir,
Thanks for your reply.
I have used this .mdp file. Is there anything wrong in the mdp file which I
am using ?
To tell you in detail : First I have done energy minimization. Output of
this step (box_em.pdb) is used to create an index group for sol and cl- ions
using make_ndx. Then I am
Pawan Kumar wrote:
Hello sir,
Thanks for your reply.
I have used this .mdp file. Is there anything wrong in the mdp file
which I am using ?
No, but the manner in which you are using groups in that .mdp file isn't
consistent with the way you've defined them in your index file - like I
said
Hello all,
Due to the recent influx in questions related to membrane proteins (especially
with common questions), I decided to put together a step-by-step tutorial for
membrane protein systems. It's a work in progress, so I would genuinely
appreciate feedback from anyone who has a few
Your system is exploding, i.e. you have severe atomic overlap somewhere. Having
no idea what you've done to construct your system, it is hard to give any useful
advice. It is probably best if you search the list archive for variable ci
(it will return many useful posts) or search the wiki
hello users
I am starting a membrane protein simulation. I had some missing residues in the
protein which have been added now. Should I minimise in vaccum before insertion
of the protein in bilayer?
Another question : Is it necessary to do simulation in water before inserting
protein nto
hello users
I am starting a membrane protein simulation. I had some missing residues
in the protein which have been added now. Should I minimise in vaccum
before insertion of the protein in bilayer?
That depends how bad the new residue coordinates are, and whether vacuum
EM is better than
Quoting pragya chohan [EMAIL PROTECTED]:
hello users
I am starting a membrane protein simulation. I had some missing residues in
the protein which have been added now. Should I minimise in vaccum before
insertion of the protein in bilayer?
Couldn't hurt, but probably not necessary.
this file. After all , am I right?
Happy new year,
Behnoush
- Original Message -
From: Yanzi Zhou [EMAIL PROTECTED]
To: Discussion list for GROMACS users gmx-users@gromacs.org
Sent: Saturday, December 22, 2007 11:37:59 PM (GMT+0330) Auto-Detected
Subject: Re: [gmx-users] Membrane protein simulation
Dear Behnoush:
Dear Yanzi,
Of course the system charge is 30+ so I have to add 30 Cl- . So I put “nn 30” to the command like this:
genion -s protein_pope_em.tpr -o protein_pope_ion.pdb -nname CL- -nn 30 -g protein_pope.log
But it seems only one water has been replaced with Cl-. Do I have to
Dear Yanzi,
Forthunatly my simulation was run. this time I select the pope files of the Dr
Tieleman's site and create the protein_in_pope.pdb with ffgmx force field.
Then I ran genbox to solvate the system and delete some pope which had crash
with the protein.Also I added #include lipid.itp in
Eric Jakobsson wrote:
npt, but permit the box to change dimensions independently in the
three directions in response to that component of the virial.
Does it really matter whether one uses semiisotropic p-coupling or
independent coupling in x and y? Are there any examples where
semiisotopic
On Mon, 17 Dec 2007 09:02:19 +0100
Jochen Hub [EMAIL PROTECTED] wrote:
Eric Jakobsson wrote:
npt, but permit the box to change dimensions independently in the
three directions in response to that component of the virial.
Does it really matter whether one uses semiisotropic p-coupling or
Dear Behnoush:
The first three lines of popc.itp is not the problem. I got these in
pope.itp.
Could you attach your input files?
Best regards.
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Please
Thanks Yanzi,Thanks Mark,
for your very usefull points,
I have another pdb2gmx running on thr protein.pdb with ffgmx force
filed(matching with lipid.itp).
Also I have removed the including ffG43a1 from the lipid.itp and then running
grompp. The new errors are:
ERROR 1 [file popc.itp, line 3]:
Behnoush Zare wrote:
Thanks Yanzi,Thanks Mark,
for your very usefull points,
I have another pdb2gmx running on thr protein.pdb with ffgmx force
filed(matching with lipid.itp).
Also I have removed the including ffG43a1 from the lipid.itp and then running
grompp. The new errors are:
ERROR 1
Dear Mark,
Sorry about that mistake, the popc.itp file is began with these 3 lines:
;[ moleculetype ]
; Name nrexcl
POPC 3
the error is:
ERROR 1 [file popc.itp, line 3]:
Incorrect number of atomtypes for dihedral (1 instead of 2 or 4)
Fatal error:
Bonded/nonbonded atom type '1' not
Behnoush Zare wrote:
Dear Mark,
Sorry about that mistake, the popc.itp file is began with these 3 lines:
;[ moleculetype ]
This is a comment before a directive that tells grompp that this is
going to be a new molecule type. Hence, it thinks it's in the old one,
and that this should be part
npt, but permit the box to change dimensions independently in the
three directions in response to that component of the virial.
At 11:43 AM 12/16/2007, you wrote:
Dear User
I am starting a membrane simulation. Is it advisablr to complete all
runs in npt or nvt?
Pragya Chohan
--
Dear Yanzi,
Thank you for your swift response. I did all you wrote to me. Also I include
ffG43a1 forcefield in the lipid.itp file and then include the lipid.itp file in
the protein.top at line 12 as forcefield parameter. When I run grompp the
following error appeared:
Fatal erroe; Invalid
Dear Behnoush:
I think it is because the lipid.itp is a mixture of lipid and ffgmx
parameters. Different force field uses different labels for molecules
and atoms. Try using ffgmx instead of ffg43a1, and find out if the
problem will be resolved.
Sincerely, Yanzi
I am trying to set up an ED experiment with the low resolution structure of a
membrane protein in the hope of generating NMR-like structures.
By ED do you mean essential dynamics? I haven't done that, but it
seems to me that the system setup should be identical to regular MD.
From what I
Title: membrane protein simulation
Hi gmx-users
I am trying to set up an ED experiment with the low resolution structure of a membrane protein in the hope of generating NMR-like structures. >From what I have read until now, I know that I should either restrain the transmembrane domain of
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