hi
i am simulating a membrane protein in POPC bilayer and for that i am following
justin's tutorial.it's a nice tutorial and is really helpful. but i'm facing
some problems in running the grompp command. after the solvation when i am
going to run grompp, it is generting an error as follows -
--- On Mon, 8/6/09, Justin A. Lemkul wrote:
From: Justin A. Lemkul
Subject: Re: [gmx-users] problem in running grompp
To: "Discussion list for GROMACS users"
Date: Monday, 8 June, 2009, 4:47 PM
Samik Bhattacharya wrote:
> hi
> i am simulating a membrane protein in POPC
hi, i am simulating a membrane protein inside dppc bilayer and in this regard i
am following justin's tutorial. but i ma facing a problem in running
grompp...whenever i run it is giving error
Program grompp, VERSION 4.0.5
Source code file: grompp.c, line: 362
Fatal error:
number of coordinates
hi,
Justin, i have completed upto the genion step of that simulation. One error is
creeping in this step which is nonzero system charge. my system is said to have
a charge 1.69. now how to neutralize this kind of broken charge? another thing
is that how this kind of broken chage is being develop
hi i'm simulating a ion channel protein in DPPC membrane. i'm following
Justin's tutorial for that. and have completed upto the solvation step. but
right after solvation, i found some water molecules in the channel. now i want
to delete those molecules. in the tutorial it is advised tyo use the
em?
thanks again
Shamik
On Fri, Jul 3, 2009 at 8:08 PM, Samik Bhattacharya wrote:
> hi i'm simulating a ion channel protein in DPPC membrane. i'm following
> Justin's tutorial for that. and have completed upto the solvation step. but
> right after solvation, i found s
hi,
I am running a simulation of a membrane protein in DPPC bilayer. ii have
completed upto genion step. But when i am going to minimize the energy of the
system the mdrun crashes showing
Stepsize too small, or no change in energy.
Converged to machine precision,
but not to the requested precisi
Hi all, i ma simulating a membrane protein, in which i am facing a problem in
the equilibration step. in the NVT equilibration when i am running the mdrun
command i am getting a msg like
Program mdrun, VERSION 4.0.5
Source code file: constr.c, line: 136
Fatal error:
Too many LINCS warnings (19
--- On Wed, 15/7/09, Mark Abraham wrote:
From: Mark Abraham
Subject: Re: [gmx-users] Lincs Warning
To: "Discussion list for GROMACS users"
Date: Wednesday, 15 July, 2009, 5:23 PM
Samik Bhattacharya wrote:
> Hi all, i ma simulating a membrane protein, in which i am facing a prob
--- On Thu, 16/7/09, Justin A. Lemkul wrote:
From: Justin A. Lemkul
Subject: Re: [gmx-users] Lincs Warning
To: "Discussion list for GROMACS users"
Date: Thursday, 16 July, 2009, 7:30 AM
Samik Bhattacharya wrote:
>
>
> --- On *Wed, 15/7/09, Mark Abraham //* wrote:
>
hi, i am simulating a peptide in lipid bilayer where i've completed the
production run. but the problem is that i cant install grace as it requires
motiff api. a have installed lesstiff but still when i am going to intall grace
its again complaining theat it could not find motiff api. it'll be g
hi, i'm simulating a membrane protein in DPPC bilayer. here i'm using
inflategro perl script. just after the first run when i'm running grompp to
minimize it i have found a large force on a phenylalanin atom which is well
over
1015
Now what to do with this one? I had a view of that p
hi alli'm facing alot of trouble in installing grace in my redhat machine. its
always complaining about Motiff API. ive installed Lesstiff but even afetr that
grace is not getting installed...i can't make out how to install it? is there
any problem in the path? should i've to set path before gr
--- On Mon, 27/7/09, Morteza Khabiri wrote:
From: Morteza Khabiri
Subject: [gmx-users] POSITION-RESTRAIN
To: gmx-users@gromacs.org
Date: Monday, 27 July, 2009, 7:35 PM
Dear gmxusers.
I want to restrain the lipids in my system which contains protein,lipid
and water. I make the restraint itp f
hi i have completed the process of simulating a protein in a lipid
environmant... now in the analysis part i have generated some graphical
representations of the angle, RMSD etc. but from that i cant conclude about the
success of the simulation.is there any thing (research papers, namely)
w
--- On Mon, 3/8/09, Justin A. Lemkul wrote:
From: Justin A. Lemkul
Subject: Re: [gmx-users] analysis of result
To: "Discussion list for GROMACS users"
Date: Monday, 3 August, 2009, 5:03 PM
Samik Bhattacharya wrote:
> hi i have completed the process of simulating a prote
--- On Mon, 3/8/09, Justin A. Lemkul wrote:
From: Justin A. Lemkul
Subject: Re: [gmx-users] analysis of result
To: "Gromacs Users' List"
Date: Monday, 3 August, 2009, 8:23 PM
Samik Bhattacharya wrote:
>
>
> --- On *Mon, 3/8/09, Justin A. Lemkul //* wrote:
&g
--- On Thu, 13/8/09, st wrote:
From: st
Subject: [gmx-users] problem installing gromacs
To: gmx-users@gromacs.org
Date: Thursday, 13 August, 2009, 1:42 AM
Hi There,
I have some problems
installing gromacs on the linux server.
fftw installed with no error, but when I install
gromacs
hi all, i am analyzing a trajectory of a membrane protein embedded in DMPC
bilayer. for this i'm using deuterium order analysis where i have created two
different index groups for the acyl chains. now when i am running g_order its
giving an error message like
Program g_order, VERSION 4.0.5
So
--- On Mon, 31/8/09, Justin A. Lemkul wrote:
From: Justin A. Lemkul
Subject: Re: [gmx-users] error in Deuterium order analysis
To: "Discussion list for GROMACS users"
Date: Monday, 31 August, 2009, 7:25 PM
Samik Bhattacharya wrote:
> hi all, i am analyzing a trajectory
hi all,
i have simulated a membrane protein system in DPPC and DMPC bilayer. i have got
the trajectories and analysed them with the gromacs tools. now i want to get
the bonding connectivity of the protein with that of the lipid layer. can i get
that graphically (i.e. in xvg format) ? is there an
hi
i am new to Gromacs. i want to simulate a protein inside a lipid box(preferably
POPC or POPE). i have generated the protein inside the POPC box complex. But
whenever i am going to build the .gro and .top file of that complex with
pdb2gmx an error is creeping in saying "Cant find POP in residu
available in the topology database in
gromacs.
So the starting point would be to generate a topology and a gro file for the
protein alone as such and then edit the topology to include the .itp files as
specifically needed for the lipids.
Regards,
Pawan
On Fri, May 22, 2009 at 4:42 PM, Samik
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
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
hi,I
i am facing a lot of troubles in installing Gromacs in my Redhat machine..I've
followed all the instructions given in the manual as well as in the website.
ialso have installed fftw,its compiling with no problem. . but whenever i run
pdb2gmx or command lke that its giving an error "comman
hi i am simulating a membrane protein where i am facing some difficulties in
running the inflategro.pl available at http://moose.bio.ucalgary.ca. i cant
understand what should be the input of areaperlipid.dat file? where can i find
that file ? or i've to make it myself? also contents of the sam
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