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 g_
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 dist
Hello,
I've carried out simulation of a protein embedded in a membrane using
the MARTINI coarse-grained force field. My simulation is 1 micro
second long and towards the end of the simulation the protein drifts
towards the 'edge' of the box.
In my analysis, I want to look at the minimum
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" wrote:
>
>
> Michael Daily wrote:
>> Unfortunately genbox will put waters anywhere there is a space,
>> including i
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
di
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
run
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 resu
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 position
Thanx Justin...i must go throuh that tutorial. thanx for the help.
--- On Fri, 29/5/09, Justin A. Lemkul wrote:
From: Justin A. Lemkul
Subject: Re: [gmx-users] membrane protein simulation
To: "Discussion list for GROMACS users"
Date: Friday, 29 May, 2009, 4:49 PM
Samik Bhattach
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 a
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 a
>
> 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 t
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. R
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 bilay
file. After all , am I right?
Happy new year,
Behnoush
- Original Message -
From: "Yanzi Zhou" <[EMAIL PROTECTED]>
To: "Discussion list for GROMACS users"
Sent: Saturday, December 22, 2007 11:37:59 PM (GMT+0330) Auto-Detected
Subject: Re: [gmx-users] Membrane protein
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 repe
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 repeat
this ste
Dear Behnoush:
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 #includ
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
Diane,
how big is the transmembrane part of your protein?
Diane Fournier wrote:
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
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 hav
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 th
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