Dear GMX Users,
I am wish to perform a conformational transition simulation using
coarse-grained models (SBM http://smog-server.org/). I wanted to apply flooding
to explore the conformational transition and have open-close transition my
trajectory. But what I find is that when I start from a
Dear GMX Users,
I am wish to perform a conformational transition simulation using
coarse-grained models (SBM http://smog-server.org/). I wanted to apply flooding
to explore the conformational transition and have open-close transition my
trajectory. But what I find is that when I start from a
Dear GMX Users,
I performed an ANM calculation at
http://ignmtest.ccbb.pitt.edu/cgi-bin/anm/anm1.cgi
It returned me eigenvectors in the following format (where the second and
third column represent first and second eigenvector)
1 0.010551 -0.048553
1 -0.022038 -0.042918
1 0.107906
Sorry to bother you all once again. As there were no replies, I assume it is
not possible to implement COM distance restraints in a way similar to distance
restrains.
nahren
From: nahren manuel meetnah...@yahoo.com
To: gromacs gromacs gmx-users@gromacs.org
Dear Gromacs Users,
I was wondering if there is a way to implement the COM distance restraints
(which I presently apply using pull, and setting pull-rate =0.0) in way similar
to distance restraints defining the lower up1 up2 (i.e harmonic restraint with
a flat well). Any suggestion will be
Dear Gromacs Users,
I am trying to study ligand unbinding adopting Umbrella sampling (using Gmx
4.5.3). during my initial pull to generate configurations for umbrella windows
I have pulled in the -Z direction,
@ s0 legend 0 Z
@ s1 legend 1 dZ
0. 7.37361 -0.33625
0.0200 7.37377
, approx. 1 ns runs in 5 windows)
Best,
nahren
From: Justin A. Lemkul jalem...@vt.edu
To: nahren manuel meetnah...@yahoo.com; Discussion list for GROMACS users
gmx-users@gromacs.org
Sent: Friday, November 4, 2011 7:44 PM
Subject: Re: [gmx-users] PMF when
Dear Gromacs Users,
I am trying to study the free energy of binding in a protein-ligand complex.
I use the following pull input in my mdp file:
; Pull code
pull = umbrella
pull_geometry = distance
pull_dim = N Y N
pull_start = yes
pull_ngroups = 1
Dear GMX users,
I am trying to center my protein at the center of box using editconf. When I
view the same using ngmx, the protein seems to lie outside the box
neweditconf -f alapdb.pdb -bt cubic -o boxpdb.pdb -c -center -0.156 -0.061
0.084 -d 1.5
this one works, but the molecule is shifted.
Dear Gromacs Users,
Is it possible to get the forces (components, x,y, z) acting on each atom from
the simulation or from the rerun.
I need them to calculate the Hessian
Similar to
http://www.sciencedirect.com/science/article/pii/S0006349507715989
Best,
nahren
--
gmx-users mailing list
Dear Gromacs Users,
I was just wondering if the formula and the units which I use for getting the
entropy is absolutely correct.
The eigenfrequency (v) in cm-1 are obtained from eigenfreq.xvg.( GMX ver 4.0.7,
using normal mode calculations)
TS = [alpha/exp(alpha)-1] - log[1-exp(-alpha)]
Dear Gromacs Users,
I am calculating entropy from QHA and Schlitters formula to determine the
entropy change in my proteinA-proteinB complex.
Since proA and proB are quite different in terms of number of residues, I am
little confused if I should divide the entropy value with the number of
Dear Gromacs Users,
I am simulating a Membrane protein, the extracellular domain alone (since the
structure of only extracellular domain is solved). So I will have to simulate
the protein in such a way that only the translational motion is allowed but the
rotational motions are prevented
Date: Thursday, November 11, 2010, 4:14 PM
nahren manuel wrote:
Dear Gromacs Users,
I am simulating a Membrane protein, the extracellular domain alone (since the
structure of only extracellular domain is solved). So I will have to simulate
the protein in such a way that only
Dear Gromacs Users,
I am using ver 4.5.1.
I completed a 500 ps run of NPT (the mdp file is below). after when i try to do
a prod run with both velocity and pressure read from the output of NPT, I get a
error
newgrompp -f eq3npt.mdp -o eq3npttpr.tpr -p dimertop.top -c eq2nptpdb.pdb -t
Dear Gromacs Users,
I am using plain cutoff for my 12-mer protein.
The grompp reports ARG to have a big charge group. this was also highlighted in
the following mail
http://www.mail-archive.com/gmx-users@gromacs.org/msg32098.html
I was just think if changing the charges on these atoms would
Dear Gromacs Users,
thanks for all your suggestions.
Tsjerk, I did try your idea, but unfortunately doesn't seem to work.
the pdb file is shared here :
http://www.4shared.com/account/file/ijofD83b/DIMER.html
newpdb2gmx -f DIMER.pdb -chainsep interactive -ignh
Fatal error:
Atom OXT in
...@gmail.com
Subject: Re: [gmx-users] pdb2gmx -chainsep vs -merge
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Tuesday, September 7, 2010, 12:22 PM
Hi Nahren,
Can you paste your actual command line where you used sed?
Cheers,
Tsjerk
On Tue, Sep 7, 2010 at 12:11 PM, nahren
.
Thank you.
Best,
nahren
--- On Fri, 9/3/10, Justin A. Lemkul jalem...@vt.edu wrote:
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] intermolecular distance restrains
To: Gromacs Users' List gmx-users@gromacs.org
Date: Friday, September 3, 2010, 3:18 AM
nahren manuel wrote
Dear Gromacs Users,
I am presently using gromacs4.5 beta(since I want implicit solvent). I wish to
apply intermolecular distance restraints.
To my surprise there is no merge option in pdb2gmx (although pdb2gnx -h, says
it has). So is there a new alternative to create intermolecular distance
--- On Thu, 9/2/10, Justin A. Lemkul jalem...@vt.edu wrote:
From: Justin A. Lemkul jalem...@vt.edu
Subject: Re: [gmx-users] intermolecular distance restrains
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Thursday, September 2, 2010, 8:09 PM
nahren manuel wrote:
Dear Gromacs
Dear Gromacs Users,
Thanks for your Reply.
Yes i did move forward to calculate the eigenvalues, as listed below.
1 -1.0096
2 -0.860704
3 -0.621409
4 -0.0477899
5 -7.98079e-07
6 -2.20151e-08
7 2.76454e-06
8 0.000416762
Dear Gromacs Users,
I am unable to minimize a complex protein (Trimer-Trimer complex) to even less
than Fmax=1.754e+00.
I tried few tricks like performing MD for few steps etc, but it does not yield
any results.
I am sure there must be a way out. Can you please advice.
Thanks for your
for EM and NMA?
Ran
nahren manuel wrote:
Dear Gromacs Users,
I am trying to calculate Entropy from Normal Mode Analysis.
I minimized the structure to
8.41750710592449e-09
Then I calculated the normal mode (the mdp file is given
) has 873 elements
Group 16 (a_913-1368_a_2203-2619) has 873 elements
Group 17 (a_1-456_a_1369-1785_a_457-912_a_1786-2202_a_913-1368_a_2203-2619)
has 2619 elements
Kindly advice
nahren
--- On Mon, 5/10/10, nahren manuel meetnah...@yahoo.com wrote:
From: nahren manuel meetnah
Dear Gromacs Users,
I simulated
two homologous (proteins) , and noticed after the simulation that in
one trajectory, the protein is stored as ABCXYZ and in another it is
as AXBYCZ. (where A, Z are chain information, ABC is a trimer and
to these results.
Cheers,
Tsjerk
On Mon, May 10, 2010 at 11:42 AM, nahren manuel meetnah...@yahoo.com wrote:
Dear Gromacs Users,
I simulated
two homologous (proteins) , and noticed after the simulation that in
one trajectory, the protein is stored as ABCXYZ
Dear Gromacs Users,
I am performing a MD simulation of a dimer in a dodecahedron box. The
simulation stopped after 8 ns (power cut) and i had to restart to complete it
fully to 12 ns.
I then concatenated the two trajectories using trjcat
trjconv -f promd.trr -s proem.tpr -pbc nojump -o
Dear Gormacs User,
I have now created a new tpr in which the protein is centered.
trjconv -f promd.xtc -s tprdodecasolv.tpr -center -boxcenter tric -pbc mol -ur
compact -o center.xtc
trjconv -s tprdodecasolv.tpr -fit rot+trans -f center.xtc -o fit.xtc
I see the dimer getting split in some of
Dear Gromacs Users,
I am having some trouble in viewing my molecule in VMD as a protein in
dodecahedron.
I did the following
1. trjconv -f promd.trr -o nojump.xtc -s promd.tpr -pbc nojump
2. trjconv -f nojump..xtc -s promd.tpr -o mdcenter.xtc -ur compact -pbc mol
-center -boxcenter tric
I
Dear Gromacs Users,
I am trying to simulate a protein whose Thr residues is phosphorylated.
I did the following based on the earlier query regarding the same
here is how I did it for phosphorylated Threonine.
1) open the appropriate .rtp file e.g. ffG43a1.rtp
2) make a copy of the
a porcupine plot.
Hope it helps,
Tsjerk
On Mon, Feb 2, 2009 at 6:28 AM, Mark Abraham mark.abra...@anu.edu.au
wrote:
nahren manuel wrote:
Dear Gromacs Users,
I have done PCA of my MD , I want to visually represent the motions
in
terms of porcupine plots. I came across Dynamite (web server
Dear Gromacs Users,
I have done PCA of my MD , I want to visually represent the motions in terms of
porcupine plots. I came across Dynamite (web server) for this purpose. But it
only considers 500 frames of the xtc file.
Is there any other way how i could generate porcupine plots based on
Dear Awasthi,
go through GROMACS Introductory tutorial...
trjconv -f abc.pdb -s abc.tpr -o 3frame.pdb -dump 3
You can also open the pdb file in VMD and save only the last frame
SIMPLE !
nahren
--- On Mon, 2/2/09, Shirin Awasthi shirin.mtech...@gmail.com wrote:
From: Shirin Awasthi
Dear Gromacs Users,
I have just completed one (5ns ) mdrun.
Now If i want to calculate the interaction energy between two residues, my
ligand and ASP104, how should I go about calculating the same.
The one option I know is by creating .ndx . But I did not expect this residue
to play an
Dear Vivek,
you just have to download swisspdb and open your pdb file. Thats all you got to
do and It is more than enough. If you have more than 2/3 residues missing then,
make sure the Ramachandran plots are fine. Also try a simple minimization
before begining gromacs.
nahren
--- On Tue,
Dear Gromacs Users,
I just wonder if it possible to define
rlist = 0.9
rvdw = 1.2
vdwtype = cut-off
rlist = 1.2 ; second rlist for rcoulomb
coulombtype = cut-off
rcoulomb = 1.5
I think calulation wise it doen't make a big change , but just the idea
striked me so wanted to know...
nahren
Dear Gromacs Users,
1. I calculated the partial charges of my ligand using QM. Since GROMACS
ignores the non-polar hydrogen, is it a good approximation to include the
charges as it is from QM method to my ligand heavy atoms ?.
2. should i adjust that partial charges , If so how to do the
QM to GROMACS
To: [EMAIL PROTECTED], Discussion list for GROMACS users
gmx-users@gromacs.org
Date: Friday, July 11, 2008, 7:25 PM
Quoting nahren manuel [EMAIL PROTECTED]:
Dear Gromacs Users,
1. I calculated the partial charges of my ligand using QM. Since GROMACS
ignores the non-polar
Dear Gromacs Users,
I calculated Partial Charges for my Ligand which is Positively Charged. When I
Do a 3-21G* partial charge assignment based , I get partial charge value of
1.1147 on one of the Carbon atoms. I am little confused about it. can partial
charges be greater than 1.???
Dear Gromacs USERs,
My ligand, which contains a piperazine ring needs to be positively charged
(+1).
When I assign Gasteiger charges, it comes out to be -0.336 on the Nitrogen.
But When I do a SEMI-EMPIRICAL PM3 to place my partial charge , it puts +0.733
on this atom. So does it mean it has
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