Dear all,
I am trying to simulation of membrane proteins I have a
basic question can we directly go for simulation of lipid+protein complex
without doing simulation of individually simulation of lipid bilayer
because I am facing lot of problem with topology file for lipid
It is probably best to fix your lipid bilayer problem first. Inserting
a protein won't fix the problem(s).
XAvier
On Mar 31, 2009, at 8:05, nitu sharma sharmanit...@gmail.com wrote:
Dear all,
I am trying to simulation of membrane proteins I
have a basic question can
He, Yang wrote:
Hi all users,
I need to add some dummy atoms in my case. I know that I need to include the
section [virtual_sites] in the top file but I am not sure how to define them
in the itp file .Do I need to list these atoms in the section[atoms] ? Can
anyone of you give me some
Hi there,
We are happy to announce the iCing web interface to CING
(http://nmr.cmbi.ru.nl/cing) that can validate your NMR data
structures online, running tools such as What If, Procheck, Wattos,
ShiftX, etc..
Please direct your browser to: https://nmr.cmbi.ru.nl/icing
You can send in your
Pawan Kumar wrote:
Respected Sir,
Greetings from Pawan.
I have used force constants of 10 in position restraint .itp files
for proteins as suggested in Dr. Tieleman' s webisite for Inflategro.
The mdp files are :
The .mdp files look reasonable enough, although I don't know why you are
Justin A. Lemkul wrote:
Pawan Kumar wrote:
Respected Sir,
Greetings from Pawan.
I have used force constants of 10 in position restraint .itp files
for proteins as suggested in Dr. Tieleman' s webisite for Inflategro.
The mdp files are :
The .mdp files look reasonable enough,
Respected Sir,
Greetings from Pawan.
I have edited the lipid.itp file to add just one line extra H atom from
the opls_force_filed.itp at the end of lipid interactions data and that
works fine.
I have done this after seeing the archives. It was given either I should
change the file for sigma and
Pawan Kumar wrote:
Respected Sir,
Greetings from Pawan.
I have edited the lipid.itp file to add just one line extra H atom
from the opls_force_filed.itp at the end of lipid interactions data
and that works fine.
I have done this after seeing the archives. It was given either I should
Respected Sir,
Greetings from Pawan.
Thanks for all your suggestions.
Is it possible to use the lipid.itp file from Tieleman sir's website in
combination with GROMOS 96 force field without any modification ?
Is it fine if I use the Gromos/Berger force field combination for the system
I am using ?
Pawan Kumar wrote:
Respected Sir,
Greetings from Pawan.
Thanks for all your suggestions.
Is it possible to use the lipid.itp file from Tieleman sir's website in
combination with GROMOS 96 force field without any modification ?
If you want to use lipid.itp without any modification, you are
On Tue, Mar 31, 2009 at 07:23:57AM -0400, Justin A. Lemkul wrote:
Force fields have to be internally self-consistent, so using the parameters
from OPLS with Berger lipids will give spurious results. The only proper
combinations are Gromos/Berger or OPLS/converted Berger.
as long as one
Respected Sir,
Greetings from Pawan.
Thanks for all your kind help and suggestions.
I will work on this and ask you if I have further doubts.
Is it fine if I use the perl code given in
wiki.gromacs.org/membrane-simulations for solvation after the genbox step to
remove extra waters from the
Respected Marc Sir,
Thanks for your information.
Thanking you,
Pawan
On Tue, Mar 31, 2009 at 5:31 PM, Marc F. Lensink lens...@bigre.ulb.ac.bewrote:
On Tue, Mar 31, 2009 at 07:23:57AM -0400, Justin A. Lemkul wrote:
Force fields have to be internally self-consistent, so using the
Pawan Kumar wrote:
Respected Sir,
Greetings from Pawan.
Thanks for all your kind help and suggestions.
I will work on this and ask you if I have further doubts.
Is it fine if I use the perl code given in
wiki.gromacs.org/membrane-simulations
http://wiki.gromacs.org/membrane-simulations for
Dear all,
Please find topologies (.itp files) for the lipids DPPC, DMPC, POPC and POPG
for the GROMOS96 53a6 force field in the User
Contributions-Downloads-Topologies-Molecule Topologies section
When using these files please cite:
Kukol, A., 2009. Lipid models for united-atom molecular
Dear users,
I would like to know if andersen thermostat is fully functional in the
current version of GROMACS, since I've found no available documentation.
Thanks for your help,
Camilo
___
gmx-users mailing listgmx-users@gromacs.org
Hi Justin
Thanks for your answer.
I had check the relevant sugar, but I still have the problem of
parameterization of the open GLC ring that forms the lactitol molecule.
If you know of a similar example please let me know.
Thanks very much
Carmen
ceste...@unsl.edu.ar wrote:
Hi All
I am trying
ceste...@unsl.edu.ar wrote:
Hi Justin
Thanks for your answer.
I had check the relevant sugar, but I still have the problem of
parameterization of the open GLC ring that forms the lactitol molecule.
Hence why parameterization is difficult :) But I maintain that all of the
relevant
How about MOPAC to calculate the charges for 3-methyladenine (this molecule
has a charge +1) for using the G43a1 force field?.
--
From: Ran Friedman, Biochemisches Inst. r.fried...@bioc.uzh.ch
Sent: Friday, March 27, 2009 2:35 PM
To:
How can you test the ligands when you don't know if they REALLY bind to
the protein?
--
From: Ran Friedman, Biochemisches Inst. r.fried...@bioc.uzh.ch
Sent: Friday, March 27, 2009 2:35 PM
To: bije...@yahoo.com.br; Discussion list for GROMACS users
Lucio Montero wrote:
How can you test the ligands when you don't know if they REALLY bind
to the protein?
Sounds like a job for docking and/or binding energy calculations.
-Justin
--
From: Ran Friedman, Biochemisches Inst.
Lucio Montero wrote:
How about MOPAC to calculate the charges for 3-methyladenine (this
molecule has a charge +1) for using the G43a1 force field?.
That may not be a bad place to start, but any parameters applied to a Gromos
molecule have to reproduce condensed phase thermodynamic
On Mon, Mar 30, 2009 at 3:23 PM, Joshua Adelman jadel...@berkeley.eduwrote:
I am interested in potentially using gromacs to do some calculations on an
C-alpha based elastic network model of the protein that I'm working on. I'm
curious if other users have done similar types of calculations, and
Hi,
I get good conservation when running NVE in gromacs with 4 fs when I use
PME-switch for electrostatics but not so good when I use switch. Any
thoughts why that would be? Params shown below.
Thanks,
Ilya
;
; File 'mdout.mdp' was generated
; By user: ichorny (502)
; On
Joe Joe wrote:
Hi,
I get good conservation when running NVE in gromacs with 4 fs when I use
PME-switch for electrostatics but not so good when I use switch. Any
thoughts why that would be? Params shown below.
Finite cutoffs (such as used with switch) are intrinsically unlikely
to conserve
Respected Sir,
Greetings from Pawan.
Thanks for your information.
Thanking you,
Pawan
On Tue, Mar 31, 2009 at 5:50 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Pawan Kumar wrote:
Respected Sir,
Greetings from Pawan.
Thanks for all your kind help and suggestions.
I will work on this
I have done the docking with autodock, and I want to do a MD satrting from the
docked position.
Mensaje citado por Justin A. Lemkul jalem...@vt.edu:
Lucio Montero wrote:
How can you test the ligands when you don't know if they REALLY bind
to the protein?
Sounds like a job for docking
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