Dear users,
I am using gromacs to understand the protein-protein
complex interaction stability prediction. for this I have used
protein-protein docked complex as initial .pdb file to simulate. According
to gromacs drug enzyme complex 3.3.1 tutorial, the .itp file needed as input
f
On 8/04/2010 5:01 PM, pawan raghav wrote:
Dear users,
I am using gromacs to understand the protein-protein
complex interaction stability prediction. for this I have used
protein-protein docked complex as initial .pdb file to simulate.
According to gromacs drug enzyme complex 3.
Oxide slab of approx. 8-9 molecules in
> length and 4-5 molecules wide just as to mimic a rigid metal slab for
> further interaction studies. Can gromacs library support this and how I
> can do that...
>
> All suggestions are welcome.
>
>
>
> Thanks
>
>
>
> Radhika
On 8 Apr 2010, at 00:45, Fernando E. Herrera wrote:
I am doing some molecular dynamics simulations of membrane systems
and i would like to ask you if someone know or have a code for the
calculation of the lateral pressure profile from the data obtained
doing membrane simulations.
You can
On 8/04/2010 5:24 PM, Ozge Engin wrote:
Hi Ravi,
I had a similar problem to yours when I was dealing with simulation of a
peptide channel. I had the crystal structure of the channel consisting
of crystal water molecules and the peptide channel. I energy minimized
the system. Although nothing see
Hello, I installed the gromacs4.0.5, when I made, it had lots of mistakes,
below is some of the mistakes:
In file included from ngmx.c:50:
Xstuff.h:48:22: error: X11/Xlib.h: No such file or directory
Xstuff.h:49:23: error: X11/Xutil.h: No such file or directory
Xstuff.h:51:28: error: X11/cursorf
On 8/04/2010 5:52 PM, kecy...@sina.com wrote:
Hello, I installed the gromacs4.0.5, when I made, it had lots of
mistakes, below is some of the mistakes:
You should prefer to install the latest version, not one that's over a
year old. Bugs get fixed...
Unless you're planning to use ngmx you c
Hi,
please I'm trying to measure an hbond between 2 specific atoms. When I used
g_hbond I didn't the result I expected because it doesn't specify the atoms
that constitute the H bond.
Now I'm trying with g_dist but I encountered a problem: when I do the
following in my index file:
r 172 & a HD2
Hi,
I am trying to do normal mode analysis on a protein having 6398 atoms. I
energy
minimized the structure using steepest descent followed by L-BFGS minimization
technique
. The Fmax was equal to 9.67927896882578e-07.
I then went on to perform normal mode analysis. The command was
nohup md
LinkedIn
Sarath Kumar Baskaran requested to add you as a connection on
LinkedIn:
--
Chinmay,
I'd like to add you to my professional network on LinkedIn.
- Sarath Kumar Baskaran
Accept invitation from Sarath Kumar Baskaran
http://www.linkedin.
Thanks Justin,
I have followed the How- tos/Polymers for creating rtp entries
for polyacrylates/acids and have been able to run MD simulations
successfully reproducing results from prior literature.
Tabulated potentials section is also sure to help gmx-users. Thanks!
Dr. M.S Sulatha
IIT-Madras,
Carla Jamous wrote:
Hi,
please I'm trying to measure an hbond between 2 specific atoms. When I
You won't be able to. A hydrogen bond is defined as occurring between 3 atoms
(D-H...A) for geometric reasons, so you have to specify at least three atoms for
the analysis.
used g_hbond I did
Dear Dr. Mark,
Thanks very much for pointing out that GROMACS can handle multiple instances
of the parameters with different n for a single dihedral.
However, given that, in the existing ffamber ports in GROMACS the other
dihedral parameters have been converted to RB form, would it make a
differ
Hi
Thanks for your response, I am allowing the two groups (frozen and
non-frozen) groups interact each other, i guess i am getting the energy of
total system from g_energy.
I checked the velocities of frozen group atoms, they are not "zero". I have
seen in git master that this problem was fixed a
Dear gmx-users,
I have generated 40ns trajectories for DPPC bilayer - water system. The
whole 40ns was generated in small trajectories and finally I concatenated
all the small trajectories to a big 40 ns trajectory using the following
options in trjcat
trjcat -f -o -settime -tu
Now the p
During configuration, there is something about xml.
a functions in analysis
--without-xml do not link to the xml2 library, disallows the
use of certain file formats
1. which file formats did they specify to?
2. Can gromacs handle the PDBML file?
Thanks and regards,
lina
<>-
On 2010-04-08 17.39, #ZHAO LINA# wrote:
During configuration, there is something about xml.
a functions in analysis
--without-xml do not link to the xml2 library, disallows the
use of certain file formats
1. which file formats did they specify to?
none.
2. Can gromacs hand
If you are working with a two-protein complex, you don't need PRODRG.
You can create the complex topology in pdb2gmx using as input a PDB file
with two chains, each chain for a protein. Then pdb2gmx does the job of
creating an itp file for each protein, and a top file for the complex,
which has #in
Dear sir :
I want to a pentamer membrane protein, when I used InflateGRO.pl with DOUGHNUT
Mode, the results were wrong, please help me!
show " [u...@localhost protein-tutorial]$ perl inflategro.txt kkr.gro 4 POPC 14
kk_inflated.gro 5 area.dat doughnut protein_subunits
Doughnut mode activated.
xi zhao wrote:
Dear sir :
I want to a pentamer membrane protein, when I used InflateGRO.pl with
/DOUGHNUT Mode, the results were wrong, please help me! /
If you want any useful help, you'll have to do a whole lot better than simply
saying "the results were wrong." No one on this list wil
1. Please include the actual commands that you used via copy and paste
so that we can see *exactly* what you did.
2. Please include a snippit of the *actual* output identifying where
the difference is that you mention here.
3. Note that g_density has some limitations, all related to volume
Please keep all Gromacs-related correspondence on the gmx-users list. I cannot
serve as a private tutor, and I do get numerous requests. You stand a much
better chance of reaching someone with useful advice by posting to the list. I
have a few ideas (see below), so I am CC'ing the list to b
On 8/04/2010 10:32 PM, Vigneshwar Ramakrishnan wrote:
Dear Dr. Mark,
Thanks very much for pointing out that GROMACS can handle multiple
instances of the parameters with different n for a single dihedral.
I hope I'm right there. There's been discussion on such topics before.
There's some subtl
Hi,
Right, the only dihedral angles that do not allow an exact translation to
RB because of the phase are the ones involving the new parametrization for
nucleic acids. Namely, it corrects the alpha/gamma transitions to get the
populations of states right, thus avoiding the loss of helicity on th
jampani srinivas wrote:
Hi
Thanks for your response, I am allowing the two groups (frozen and
non-frozen) groups interact each other, i guess i am getting the energy
of total system from g_energy.
I checked the velocities of frozen group atoms, they are not "zero". I
have seen in git mas
Dear Justin,
Thanks for your responce. Here is my mdp file.
+++
title = AB2130
cpp = /usr/bin/cpp
constraints = all-bonds
integrator = md
dt = 0.004 ; ps !
nsteps = 2500 ; total 100.0 ns.
nstcomm
jampani srinivas wrote:
Dear Justin,
Thanks for your responce. Here is my mdp file.
+++
title = AB2130
cpp = /usr/bin/cpp
constraints = all-bonds
integrator = md
dt = 0.004 ; ps !
nsteps = 2500 ; t
Hi gmx-users
I am running a simulation on protein mutant that contains a cysteine with a
MTSET (methanethiosulfonate ethyltrimethyl ammonium OR
2-(trimethylammonium)ethyl methanethiosulfonate). since its not a standard
residue or solvent there are no parameters in the gromos force field. Yet
the m
Dear Justin,
I am sorry for the poor description of the problem, OK let me explain you
clearly here.
I have taken a decapeptide and solvated it with box size 6.0 nm, I want to
create a frozen wall (confined sphere) around protein after a certain radius
(in this case it is 2.5 nm). To achieve t
On Tue, Apr 6, 2010 at 5:05 PM, Justin A. Lemkul wrote:
>
>
> Arun kumar V wrote:
>
>> Try PRODRG server to build the molecule as well as to get topology file.
>> Though you might have to be careful in using this topology file.
>>
>>
> If by "be careful" you mean "don't use this topology," I'll
I would like to run a simulation of a pentamers in a POPC membrane, and using
new inflategro with doughnut mode, but I have met similar result as the links
http://lists.gromacs.org/pipermail/gmx-users/2010-January/047977.html ,I also
got a lot of errors about uninitialized values. When the s
On 9/04/2010 1:25 PM, jampani srinivas wrote:
Dear Justin,
I am sorry for the poor description of the problem, OK let me explain
you clearly here.
I have taken a decapeptide and solvated it with box size 6.0 nm, I want
to create a frozen wall (confined sphere) around protein after a certain
rad
On 9/04/2010 1:21 PM, Evelyne Deplazes wrote:
Hi gmx-users
I am running a simulation on protein mutant that contains a cysteine
with a MTSET (methanethiosulfonate ethyltrimethyl ammonium OR
2-(trimethylammonium)ethyl methanethiosulfonate). since its not a
standard residue or solvent there are no
Hi ALL,
Is there any way in GROMACS to join two peptide chains by forming a peptide
bond between the C and N atoms?
Any suggestion is welcome.
Regards,
Anirban
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at htt
HI
how to calculate SASA of micelle using g_sas?
i put -n -micelle-index.ndx , where micelle-index.ndx includes all of the
atom numbers of micelle.
if micelle is not compact enough but there are no water molecules inside the
micelle, will g_sas calculate the vacancy part inside the micelle?
Or,
Hi all
I would like to know whether Random Accelerator Molecular Dynamics is
available in Gromacs as it is available in AMBER.
E R Azhagiya singam
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at http://www.gro
36 matches
Mail list logo
