Dear Users,
Are there any tool for superposing the trajectory
structures form MD. Please correct me if I am asking
any illogical question.
My previous question was regarding the trjconv output
pdb trajectory, is there a way to superpose all these
structures?
Thank you
With regards
M. Kavyashree
trjconv -fit rot+trans
Cheers,
Tsjerk
On Jun 23, 2011 8:12 AM, Kavyashree M hmkv...@gmail.com wrote:
Dear Users,
Are there any tool for superposing the trajectory
structures form MD. Please correct me if I am asking
any illogical question.
My previous question was regarding the trjconv output
Thank you Sir!
With regards
M. Kavyashree
On Thu, Jun 23, 2011 at 11:50 AM, Tsjerk Wassenaar tsje...@gmail.comwrote:
trjconv -fit rot+trans
Cheers,
Tsjerk
On Jun 23, 2011 8:12 AM, Kavyashree M hmkv...@gmail.com wrote:
Dear Users,
Are there any tool for superposing the trajectory
Dear Sir,
It will be of great help to send the force field. actually I want to know
whether it was working fine for u or not ?? ... Pls send the file and if
it's working fine then I think you can deposit it in User contributions in
gromacs repository...
On Thu, Jun 23, 2011 at 2:38 PM,
Hi,
That is the problem. Yet i do not know whether it is working fine
not.i have been working with that for nearly 9-10months but not
satisfied yet.
In the following mail i will cut and paste the force field parameters which
you can use it with amber. If you have time please go ahead and
ok sir..
On Thu, Jun 23, 2011 at 4:06 PM, Ramachandran G gtr...@gmail.com wrote:
Hi,
That is the problem. Yet i do not know whether it is working fine
not.i have been working with that for nearly 9-10months but not
satisfied yet.
In the following mail i will cut and paste the force
For the GFP chromophore i name residue as CRIH.
1. aminoacids.rtp
CB2 CB 0.019103 1
CA2 CC-0.026635 2
N2 NB-0.436463 3
C1 CC 0.302706 4
N3 NB-0.541478 5
C2 C 0.563844
For ffbonded.itp, i added the following. (you need to be carefull here since
i cooked upto the force constants)
C CCCBCA9 180.0 4.309 1
NBCCC O 9 180.0 4.309 1 ;
NBCCCBCA9 180.0 4.309 1
NBCCCBH29 180.0
more parameters - ffbonded.itp
NBCT 10.1444294553.6
NBC10.1404334720.0
C CC 10.1407343088.0
CCCB 10.1474468608.0
CB H2 10.1076129960.25
to aminoacids.hdb
1 1 HE2 CE2 CZ CD2
1
these are in continuity I mean for the ffbonded.itp file
On Thu, Jun 23, 2011 at 4:21 PM, Ramachandran G gtr...@gmail.com wrote:
more parameters - ffbonded.itp
NBCT 10.1444294553.6
NBC10.1404334720.0
C CC 10.1407343088.0
CCCB
yes!
On Thu, Jun 23, 2011 at 12:26 AM, bharat gupta bharat.85.m...@gmail.comwrote:
these are in continuity I mean for the ffbonded.itp file
On Thu, Jun 23, 2011 at 4:21 PM, Ramachandran G gtr...@gmail.com wrote:
more parameters - ffbonded.itp
NBCT 10.1444294553.6
NBC
It is neutral.
I tried sending the coordinates but it bounces. So i paste below the
chromophore coordinates alone.
64CRIH CB2 948 2.946 2.849 3.832
64CRIH HB2 949 2.948 2.845 3.932
64CRIH CA2 950 2.827 2.790 3.770
64CRIHN2 951 2.795 2.778 3.639
i will try ... and will reply pack to u
On Thu, Jun 23, 2011 at 4:39 PM, Ramachandran G gtr...@gmail.com wrote:
It is neutral.
I tried sending the coordinates but it bounces. So i paste below the
chromophore coordinates alone.
64CRIH CB2 948 2.946 2.849 3.832
64CRIH HB2
Dear Sir,
I tried fitting the proteins of the trajectory in pymol
as mentioned in your (Dr. Tsjerk's) tutorial, but later
I tried using the trjconv -fit rot+trans to fit the proteins
in the trajectory as you had mentioned.
I do not observe this degree of movement in protein
when I view the
Hi Kavya,
For us to say anything sensible about it, we should at least know
exactly what you've tried. Copy-paste the commands exactly as you
issued them, and provide the parts of the output that seem relevant.
Cheers,
Tsjerk
On Thu, Jun 23, 2011 at 9:54 AM, Kavyashree M hmkv...@gmail.com
Hi,
I want to simulate a docked complex of my protein (GFP) with
phosphotyrosine. I have found this - ffG43a1p forcefield contains parameters
for pTYR, so I want to know how good is this FF for simulating my system...
As in the literature its mentioned that people have used CHARMM, AMBER, OPLS
ff
Dear Sir,
1 simulation for 100ns -
ED analysis proceeded as follows:
g_covar -s input.tpr -f .input.xtc -o eigenvectors.xvg -v
eigenvalues.trr -xpma covar.xpm
g_anaeig -s input.tpr -f input.xtc -v eigenvectors.trr -eig
eigenvalues.xvg -proj proj-evi.xvg -extr evi.pdb -rmsf rmsf-evi.xvg -first i
Hi Kavya,
For certain I do not state in my tutorial that one should use g_nmtraj
for this. It is intended for analysis of normal modes analysis, where
the eigenvalues are related to the frequencies of the harmonic
motions. You're using it on the modes with largest eigenvalues, which
are
On 23/06/2011 12:22 PM, Lishan Yao wrote:
Dear Chris and Mark,
Thank you both for the response. I did the simulation already and
Gromacs only gives me the total dH/dl.
So what's wrong with dividing by two, like I suggested last time? You've
got two events and you assert that they're
Dear Sir,
Yes it is not stated in your tutorial. I was mentioning
about the superposition of trajectory and visualization
in pymol.
Ok I will try that. Thank you for the suggestions sir.
Thanking you
With Regards
M. Kavyashree
On Thu, Jun 23, 2011 at 2:43 PM, Tsjerk Wassenaar
Please keep all Gromacs-related correspondence on the gmx-users list. I am not
a private help service. I am CC'ing this message to the list and would ask that
all further discussion take place there.
Your topology specifies dihedrals that do not exist under the desired force
field
Please don't ignore requests about proper email etiquette.
Please heed this:
When replying, please edit your Subject line so it is more
specific
than Re: Contents of gmx-users digest...
...and don't reply to the entire digest. I just stated the reasons
On 23/06/2011 7:59 PM, Lishan Yao wrote:
On 23/06/2011 12:22 PM, Lishan Yao wrote:
Dear Chris and Mark,
Thank you both for the response. I did the simulation already and Gromacs
only gives me the total dH/dl.
So what's wrong with dividing by two, like I suggested last time? You've
got
Hi everyone,
I'm simulating a bead-spring polymer model (1600 chains and 10 beads per chain
in a 26.6^3 box with pbc) with LJ and FENE potentials.
I calculate the mean-square-displacement for different temperatures. For T=0.46
(in LJ units) I expected to get a plateau in the msd curve (glass
On 23/06/2011 3:08 PM, Kavyashree M wrote:
Dear users,
In one of the simulations while calculating box dimensions
using g_energy this output was obtained -
Statistics over 5001 steps [ 0. through 10. ps ], 3
data sets
All statistics are over 1978700 points
Energy
Zack Scholl wrote:
Hi all-
Is it possible to freeze a group of atoms only partially in a
direction? For instance, could I freeze a group inside a box of a
definite size?
Not by defining a box, as such, but you can freeze any subset of atoms with a
suitable index file that defines the
Zack Scholl wrote:
Zack Scholl wrote:
Hi all-
Is it possible to freeze a group of atoms only partially in a
direction? For instance, could I freeze a group inside a box of a
definite size?
Not by defining a box, as such, but you can freeze any subset of atoms with a
suitable index file
probably yes, but you need to test that assumption.
best
Andre
On Wed, Jun 22, 2011 at 8:25 PM, Chathurika Abeyrathne
c.abeyrat...@student.unimelb.edu.au wrote:
Thank you.
If I apply an electric field will I be able to get only positive values?
Regards,
Chathurika.
2011/6/22 André
Hi all,
I am trying to measure the energy curve of unwinding the SNARE protein
complex. This requires pulling the C-termini of two helices apart from each
other, while fixing certain other parts of the complex. To do this I
excluded the reference group, so that all groups were pulled to absolute
Hello gmx-users,
I wrote a script to perform a simulation on my Ubuntu 10.04 machine
running Gromacs 4.0.7. At the beginning of the script I convert the
system from pdb coordinates to gro using pdb2gmx. I am using the
GROMOS 45a3 forcefield, specified by -ff G45a3 and it works great.
pdb2gmx -f
Keith Callenberg wrote:
Hello gmx-users,
I wrote a script to perform a simulation on my Ubuntu 10.04 machine
running Gromacs 4.0.7. At the beginning of the script I convert the
system from pdb coordinates to gro using pdb2gmx. I am using the
GROMOS 45a3 forcefield, specified by -ff G45a3 and
Dear Chris and Mark,
Thank you both for the response. I did the simulation already and
Gromacs only gives me the total dH/dl.
So what's wrong with dividing by two, like I suggested last time? You've
got two events and you assert that they're independent, so the
statistics should be
Hi,
I generated the topology and parameter file for phosphotyrosine usin Swiss
param and during minimization, it's giving 1,4 cut off error. I found that
the cut off for 2 paris of atom is more than the default value. So, in that
what shall I do??
--
Bharat
Ph.D. Candidate
Room No. : 7202A, 2nd
bharat gupta wrote:
Hi,
I generated the topology and parameter file for phosphotyrosine usin
Swiss param and during minimization, it's giving 1,4 cut off error. I
found that the cut off for 2 paris of atom is more than the default
value. So, in that what shall I do??
ok after reading the documentation, I think the problem is with the ligand
topology or parameter. For that I need to simulate the structure in vacuo
to check for any unusual changes in topology ...
On Fri, Jun 24, 2011 at 11:23 AM, Justin A. Lemkul jalem...@vt.edu wrote:
bharat gupta wrote:
bharat gupta wrote:
ok after reading the documentation, I think the problem is with the
ligand topology or parameter. For that I need to simulate the structure
in vacuo to check for any unusual changes in topology ...
A topology is a static entity; nothing about it changes. An in vacuo
Hi,
I am trying to calculate the dipole-dipole interaction energy of two charged
molecules. But, I was looking for a method/formula to do that. I have the .xtc
file from which I can calculate the dipole moment of each of the molecule using
g_dipole . But, then how will I calculate the
thanks..
On Fri, Jun 24, 2011 at 11:41 AM, Justin A. Lemkul jalem...@vt.edu wrote:
bharat gupta wrote:
ok after reading the documentation, I think the problem is with the ligand
topology or parameter. For that I need to simulate the structure in vacuo
to check for any unusual changes in
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