Hi Sara,
Assuming you have saved the script xtcrev.py:
# Get a clustered reference frame
trjconv -s md.tpr -f md.trr -o cluster.gro -pbc cluster -dump 20
# Extract the first part of the trajectory
trjconv -s md.tpr -f md.trr -n index.ndx -o 1a.xtc -e 1
# Reverse it
./xtcrev.py 1a.xtc
Hi Sara,
Make sure the first line of the script is:
#!/usr/bin/env python
Cheers,
Tsjerk
On Dec 30, 2011 1:25 PM, mohammad agha mra...@yahoo.com wrote:
- Forwarded Message - From: mohammad agha mra...@yahoo.com To:
Tsjerk Wassenaar tsjerkw@...
--
gmx-users mailing listgmx-users
Hey :)
Just some side notes. Make sure to distinguish between 'statistical
error' or 'standard error of the mean', which is a measure of how
'correct' your estimate of the average is, and the standard deviation
or the variance, which is a measure of the natural spread. The latter
is not an error!
Hi Sara,
The problem is that your micelle is formed at the end of the
trajectory. To get what you want, you need to mirror the trajectory,
follow the procedure you followed, and mirror the resulting
trajectory. I posted a piece of python code for mirroring a trajectory
a while back:
Hi Sara,
Please keep discussions on the list. I'm not your private tutor.
Whether you can do your analysis depends on the analysis you want to
do. But if your aim is analyzing the formation of the micelle, you're
probably better of reversing the trajectory.
1- trjconv -f md.trr -o md1.xtc -n
Hi Zahra,
You could first create rectangular boxes for each of the two, using -d 0.5
Then translate one over the first box vector length of the other (along x:
editconf -translate). Put the two coordinate sets together and generate a
rhombic dodecahedron for the combined set.
Cheers,
Tsjerk
On
Hi Vijayan R.,
Eigenvectors are specific up to a sign. So it's not said the start will end
up as the negative extreme. It seems your interpolation just shows what
happens in reverse.
As a sidenote, do check whether it is a biologically relevant motion, or
merely relaxation.
Cheers,
Tsjerk
On
Hi Anna,
Jumps like that are a consequence of PBC. Nothing wrong. Removing jumps
like you did is the proper treatment.
Cheers,
Tsjerk
On Dec 20, 2011 9:27 PM, Anna Marabotti anna.marabo...@isa.cnr.it wrote:
**
Dear gmx-users,
I've just finished several simulations of 4 single point mutants of
Hey :)
You could copy the state to the b-factor field:
fetch 1nmr, async=1
split_states 1nmr
for i in range(1,cmd.count_states()+1): cmd.alter(1nmr_%04d%i,b=%d%i)
delete 1nmr
spectrum b
Cheers,
Tsjerk
On Mon, Dec 19, 2011 at 7:38 AM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
Hi
Hi Michiel,
You're right there. The OP may have assumed that the numbers were
percentages, whereas they are the eigenvalues, which remain to be
divided by the total variance to get the cumulative fraction of
variance explained. The variance explained by the first ten pc's in
this case is
Hi Sara,
For calculation of the density you need the masses. Neither editconf
nor genbox uses real masses. They approximate the mass based on a list
of atom names and associated masses, which is quite crude and fails if
the atoms are not listed. Martini beads are not listed...
To get the density
Hi Vijayan R.,
What i infer from this is that the cumulative variance experienced by the
top 10 PC is hardly ~ 30 %.
Not experienced...; It's the variance captured by the first ten PC's.
a) does this imply inadequate sampling by MD or a limited conformational
change happening in the
On Thu, Dec 15, 2011 at 3:39 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Vijayan R.,
What i infer from this is that the cumulative variance experienced by
the
top 10 PC is hardly ~ 30 %.
Not experienced...; It's the variance captured by the first ten PC's.
a) does this imply
Hi Michiel,
I disagree, and so does semantics. The cumulative variance of a pc is the
variance of it plus the sum of the preceding ones. You're talking about the
cumulative fraction of the total variance.
Cheers,
Tajerk
On Dec 16, 2011 12:07 AM, Niesen, Michiel mnie...@coh.org wrote:
Date:
Hi Lina,
In addition, you can split out a specific state using:
create StateX, selection, state=X
Check out 'help create'
Cheers,
Tsjerk
On Thu, Dec 15, 2011 at 6:26 AM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
Lina,
To jump to any given state, X, just type,
set state, X
Hey :)
This is pretty incorrect... A high cosine content is an indicator of
unidirectional motion in phase space. I've elaborated on that on this
list some while ago.
Regarding your case, this means that, even if the RMSD is stable starting
from 5ns, the protein still experiences random
Hi Carla,
during my simulation, the dimer I'm simulating changed a lot.
So when I calculate with g_rms, the RMSD between my initial and my final
structure (choosing Protein-H), I get a value of 10 angstroms.
Have you made sure there are no atoms jumping across the boundaries?
g_rmsf -s
Hi Sundar,
Just add 0.748 Cl-
But you might want to go back through your workflow and the topology
resulting from it, to see how you ended up with a non-integer charge.
It is sort of unphysical.
Cheers,
Tsjerk
On Tue, Dec 13, 2011 at 11:59 AM, Sundargenesan sundargene...@gmail.com wrote:
Hi Jernej,
You can copy the charmm27.ff directory to your working directory and make
changes locally.
Cheers,
Tsjerk
On Dec 14, 2011 2:54 AM, Jernej Zidar jernej.zi...@gmail.com wrote:
Hi Mark.
How will pdb2gmx know it has to parse the monomeres.rtp file?
It can't. You must add to an
Hi Setare,
That tutorial is made for later gromacs versions, as stated at the
beginning. The naming of ions has changed since 4.0.*.
Cheers,
Tsjerk
On Dec 10, 2011 1:00 PM, Setare Jiji jj.64fh...@yahoo.com wrote:
Hi,
I am running Tutorial 1: Lysozyme in
Hey,
On a general note, assuming the frame is read in as a t_trxframe
structure called frame, the box is accessible as frame.box and is a
matrix instance, which means it's a 3x3 array, containing the
triclinic box as a lower triangular matrix. If the code says
t_trxframe *frame somewhere, rather
Hi Jose,
You're not the first one to follow the tutorial, it does state which
version to use (4.5, see introduction), and it does state how to fix the
topology: editing the file, adding the lines, using the appropriate names.
This tutorial is made to be read and to be thought over.
Of course
Hi Jose,
The references to NA+ and CL- have been changed, you can reload the
page in your browser if you care to continue. Now I still think your
statement was rather rude and showing disrespect to the time I put in
the tutorial. Apart from the reference to NA/CL you're also factually
incorrect
#!/usr/bin/env python
# Python compliant email -- Just save the content :)
Hey :)
The neatest way is using python to extract them from the XTC file :)
from struct import unpack
import sys
import os
def i(x): return sum([ord(x[j])(24-j*8) for j in range(4)])
def
Hi Chandan,
Pretty simple; you just take the smallest distance between the time
points in the periodic system.
Cheers,
Tsjerk
On Wed, Dec 7, 2011 at 6:44 PM, Chandan Choudhury iitd...@gmail.com wrote:
Dear gmx_users,
I was just wondering how the g_msd (of gmx 4.0.7) code, takes care of the
Hi Sean,
The .psf file format is for a topological desription (bonds, angles, etc),
not for coordinates afaik.
Cheers,
Tsjerk
On Dec 7, 2011 6:25 PM, Sean Law magic...@hotmail.com wrote:
Hi PyMOLers,
Can anybody tell me if there's a way to read in a protein structure file
(PSF). This is a
Hi Valerio,
Check the help for both tools. That explains it all.
Oh, and you're not correct ;)
Cheers,
Tsjerk
On Mon, Dec 5, 2011 at 4:42 PM, vferra...@units.it wrote:
Dear all,
I need to calculate the RMSD of a protein during time. So that I've
calculated the trajectory; for the
Hey :)
I think I recall there was a way to suppress writing step*.pdb files,
but I couldn't find it. Anyone know from the top of his/her head?
Otherwise I'll go and check the source...
Oh, trust me... I know what I'm doing ;) Even though it's insane... :D
Groetjes,
Tsjerk
--
Tsjerk A.
Thanks guys! I see I'm using an outdated manual...
Tsjerk
On Wed, Nov 30, 2011 at 1:28 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Mark Abraham wrote:
On 30/11/2011 9:56 PM, Tsjerk Wassenaar wrote:
Hey :)
I think I recall there was a way to suppress writing step*.pdb files,
but I
Hi Bipin,
Gromacs uses nm.
Cheers,
Tsjerk
On Wed, Nov 30, 2011 at 3:32 PM, bipin singh bipinel...@gmail.com wrote:
Hello,
Please let me know what is the unit of r (nm or A) in the radial
distribution function
output(rdf.xvg) of the program g_rdf in gromacs. As the output shows no units.
Hi Ricardo,
Unfortunately that is not possible. What you can do is rearrange the water
in the structure and use two water moleculetypes, one with and one without
position restraints. It might be nice to have something like
global_position_restraints, added under [ system ], but that needs to be
Hi Saba,
You can use g_mdmat or run g_rmsdist for different time windows.
It's also a good idea to have a look at all the analysis tools and
think of how they may suit your purpose.
Cheers,
Tsjerk
On Thu, Dec 1, 2011 at 5:43 AM, Saba Ferdous saba.bsbi...@iiu.edu.pk wrote:
Dear Sir,
I am
trjcat
Cheers,
Tsjerk
On Nov 30, 2011 6:11 AM, Saba Ferdous saba.bsbi...@iiu.edu.pk wrote:
Dear Gromacs group,
I was running simulation of protein complex, due to power outage, my
simulation got interrupted. I resumed it by the mdrun command provided. it
got resumed starting from the frame,
Hi Martin,
It should be RMSD indeed. Mind that the final RMSD from align is obtained
after optimizing the fit by leaving out outliers.
Cheers,
Tsjerk
On Nov 29, 2011 10:07 AM, Martin Hediger ma@bluewin.ch wrote:
Is the RMS the same as RMSD? PyMOL writes RMS when using align.
Martin
Hi Martin,
Here's a fourth option (and the technique worth noting :p ):
print len( set( [(i.chain,i.resi,i.resn) for i in
cmd.get_model(selection).atom] ) )
Cheers,
Tsjerk
On Tue, Nov 29, 2011 at 4:26 PM, Jason Vertrees
jason.vertr...@schrodinger.com wrote:
Hi Martin,
You get three
Hi,
You can print the moleculetype definition, up to the system tag using sed:
sed -n -e '/^\s*\[\s*system\s*\]\s*$/q' -e
'/^\s*\[\s*moleculetype\s*\]\s*$/,$p' TOP ITP
First expression: quit at [ system ], allowing spaces before, in between
and after
Second expression: print everything from [
Hi Martin,
The temporary namespace for an atom means that variables like 'resn'
can be used to refer to the attribute with that name on the atom
instance.
You are right that iterate is here used to iterate over a single atom.
That does seem a bit odd :p But it seems to be a more straightforward
My my. Why is it a fault to adhere to ISO units (nm) over non-standard
(A)? It's a choice, but a choice is not faulty. The consequences may
be undesirable. But shouldn't a user, certainly a computation
scientist, understand the file formats, as an experimentalist should
know its solvent? And know
by converting it to 0.417 nm in the gro file. What
is the point in dropping useful 2 by introducing useless 0?
On Sun, Nov 27, 2011 at 10:30 AM, Tsjerk Wassenaar tsje...@gmail.com
wrote:
My my. Why is it a fault to adhere to ISO units (nm) over non-standard
(A)? It's a choice, but a choice
to increase that time (and like everyone you will regret that decision
at least once!)
Mark
Thanks again
James
2011/11/25 Tsjerk Wassenaar tsje...@gmail.com
Hi James,
There have been extensive discussions about this on the list. Check the
archives. In short, smaller systems give
Hi Gloria,
It think it's pretty obvious that loose pieces will see one another
across periodic boundaries diffusing around the place. Whether it's a
good model of reality is something for you to verify. A priori, the
approach seems fine.
Cheers,
Tsjerk
On Fri, Nov 25, 2011 at 8:46 AM, Gloria
, Nov 25, 2011 at 10:01 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hey,
You don't actually need to copy the trajectory. trjconv and other
tools are comfortable operating on an unfinished trajectory. They'll
just bail out at the end. As an alternative, here's a python one-liner
to extract
Hi Chrysostomos,
To understand this, you have to understand how jumps are removed. I
explained that before, and it's in the archive somewhere. The bottom
line is that jumps can't be removed properly when intervals between
frames are too large, or the changes in position are too large
relative to
2011, at 18:17, Tsjerk Wassenaar wrote:
Hi Henry,
That would be a bit of a wild west approach. A better approximation
would be taking the charges from the backbone amide group, as it is
just an amide with on either side aliphatic carbons. Doing it properly
is a bit more involved
Hi Albert,
You can use the free energy perturbation stuff. Check the manual.
Cheers,
Tsjerk
On Nov 25, 2011 7:43 AM, Albert mailmd2...@gmail.com wrote:
Dear all:
I am a new Gromacs user and I would like to relax my membrane system by
linear force constant:
NPT with protein and ligand
Hi James,
There have been extensive discussions about this on the list. Check the
archives. In short, smaller systems give larger fluctuations, and shorter
simulations give larger deviations from the expected average.
Cheers,
Tsjerk
On Nov 25, 2011 7:23 AM, James Starlight
Hi Yun,
I would not have expected otherwise :p
Would you mind sharing your solution?
Cheers,
Tsjerk
On Nov 24, 2011 4:54 AM, Yun Shi yunsh...@gmail.com wrote:
Sorry for this question.
The bash script turned out to be a one-liner.
Yun
--
gmx-users mailing listgmx-users@gromacs.org
Hi [insert name here],
Try putting an empty gurgle.dat in your working directory to see if that is
the problem. If it's not, can you provide additional information regarding
your system and gromacs installation?
Cheers,
Tsjerk
On Nov 24, 2011 5:50 AM, 杨伟 20104227...@suda.edu.cn wrote:
I was
Hi Henry,
That would be a bit of a wild west approach. A better approximation
would be taking the charges from the backbone amide group, as it is
just an amide with on either side aliphatic carbons. Doing it properly
is a bit more involved, as for the G53a6 FF you need to choose
parameters giving
Hi Jose,
Check g_rmsdist -h
Not sure about the references though.
Cheers,
Tsjerk
On Nov 22, 2011 3:23 PM, Jose Borreguero borregu...@gmail.com wrote:
Dear Gromacs users,
Is there any algorithm/procedure to calculate NOEs from an MD trajectory?
I'd greatly appreciate any references where the
Hi Elizabeth,
These missing terms are filled in automatically by grompp from the
bondtypes, angletypes and dihedraltypes definitions in the *bon.itp.
Unless grompp complains about missing terms, you'll be fine. You can
check whether everything is okay by writing out a processed topology
(grompp
Hi Anushree,
I assume the rudeness of the last two sentences is unintentional. You
might benefit from reading
http://catb.org/~esr/faqs/smart-questions.html
The problem only occurs if you generated a topology by yourself or
took it from someone else. That would indicate that you're a
relatively
Hi Bipin,
It seems one of the proteins is taking longer to reach an equilibrium.
Maybe it is undergoing a conformational change?
Did you calculate the principal components per protein, or for the
joint trajectories? It would have been better to echo the commands you
used on the list, because it
Hi Troels,
I think to get the return values of a script, you need to put them
inside python boxes
I'd assume it'd be a Python script :) But also for a PyMOL script,
it's not exactly true. However, then there should be no space before
the equality sign. This should work:
theCenter=COM(...)
Hi James,
PCA on a trajectory is about fluctuations -the correlation between
deviations from an average positions-, NMA is about penalized
displacement -the increase in potential energy due to concurrent
displacement-. In NMA the lowest mode is that for which most atoms can
move most
Hi Yun,
Well, within 2 nm periodic images can influence each other through ordering
of water. But how much that will affect your results and how relevant it is
for the properties you're after is hard to tell. I think most people will
just continue with analysis, saying that there have been no
Hi Yun,
Make sure to remove jumps from the trajectory (trjconv -pbc nojump) before
using g_mindist.
Also visually check a frame that is reported to have closed contacts.
Hope it helps,
Tsjerk
On Nov 10, 2011 1:45 AM, Yun Shi yunsh...@gmail.com wrote:
Sorry, I just found that even if I use a
Hi James,
1- Can I obtain same fluctuations along ensemble of several modes (i.e
averaged fluctuations along modes from n to k ) in one graph ?
The total fluctuation is the sum of the fluctuations along all the
modes. To get what you want, you just need to some the fluctuations.
Alternatively,
Hi Steven,
Don't use -ur compact in the first step and see if that solves the problem.
Oh, and be sure that the thing is not just diffusing. There was a
thread lately where a diffusing ligand drove someone mad trying to
remove the 'jumps'.
Cheers,
Tsjerk
On Mon, Nov 7, 2011 at 3:08 PM, Steven
Hi Steven,
Step 2: Cluster your molecules.
This is where you have to forge a reference frame that you can use to
remove jumps from your trajectory. If the ligand is not with the
protein at the start, you'll have to shift it so that it is. Maybe
-pbc cluster is your friend there. I do assume that
Sure!
You'll just be looking at correlations between secondary structure
elements, disregarding the role that the loops may play. But it's a
sound approach.
:)
Tsjerk
On Tue, Nov 1, 2011 at 3:44 PM, vivek modi modi.vivek2...@gmail.com wrote:
Hi,
I plan to perform PCA on a globular protein
Hi Wendy,
Most of the binary operators can deal with matrices and vectors natively:
A-c(12,3,4)
B-matrix(c(4,10,4,13,2,8),3,2)
B
[,1] [,2]
[1,]4 13
[2,] 102
[3,]48
BA
[,1] [,2]
[1,] TRUE FALSE
[2,] FALSE TRUE
[3,] FALSE FALSE
Cheers,
Tsjerk
On Sun, Oct 30,
Hi,
To compare row wise is merely to compare column wise using the transpose matrix:
t(B) A
or
t(t(B)A)
if the result needs to be a matrix with dimensions equal to B.
Cheers,
Tsjerk
On Sun, Oct 30, 2011 at 9:44 AM, Patrick Burns pbu...@pburns.seanet.com wrote:
Given that you want to
On Fri, Oct 28, 2011 at 9:15 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Lina,
Don't combine fitting, centering and pbc options. It may not work as
expected. That's why the workflow is given. Use separate passes. By the way,
first centering on the protein followed by putting molecules
, lina lina.lastn...@gmail.com wrote:
On Fri, Oct 28, 2011 at 5:37 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Lina,
My previous reply was from before I looked at the graph. Have you
considered that the molecule might be taking a stroll and turn back,
Ha ... stroll?!
or goes to another
Hi Lina,
Make sure to use a reference in which the molecules are together (clustered)
the way you want them.
Cheers,
Tsjerk
On Oct 27, 2011 11:47 AM, lina lina.lastn...@gmail.com wrote:
Hi,
I have a problem using
trjconv_g -pbc nojump
or
trjconv_g -pbc nojump -center
I even tried the -pbc
Hi Lina,
Try a _translational_ fit on the protein, follwed by a pass with -pbc nojump
Hope it helps,
Tsjerk
On Oct 28, 2011 6:27 AM, lina lina.lastn...@gmail.com wrote:
On Fri, Oct 28, 2011 at 11:48 AM, Tsjerk Wassenaar tsje...@gmail.com
wrote: Hi Lina, Make su...
I used the initial mdrun
Vijaya,
Can you explain how you think that may help solve the problem? I think it
won't.
Tsjerk
On Oct 28, 2011 7:40 AM, vijaya subramanian vijay...@hotmail.com wrote:
-pbc atom
--
Date: Fri, 28 Oct 2011 06:34:28 +0200
Subject: Re: [gmx-users] trjconv and -pbc
Hey :)
Does the script pasted below do what you want? It does not move the
molecule(s), but it returns a list of occupied bins with the ids,
names and chains of residues in it.
Hope it helps,
Tsjerk
###
from pymol import cmd
def _bin(x,d):
d = float(d)
a,b,n =
Right, forgot to mention that the bin is given as the coordinates of
the lower corner, relative to the minimal coordinates.
Cheers,
Tsjerk
On Thu, Oct 27, 2011 at 6:02 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hey :)
Does the script pasted below do what you want? It does not move
Hi James,
Regarding PCA and NMA congruency, they are different things, unless
the energy landscape consists of a single harmonic potential well. The
principal components and the normal modes will usually correlate quite
well, but if the simulation is sampling different energy minima, there
may be
Hi Atila,
; Include chain topologies
#include complex_Protein_chain_A.itp
#include complex_DNA_chain_B.itp
; Include Position restraint file
#ifdef POSRES
#include posre_Protein_chain_A.itp
; Include Position restraint file
#ifdef POSRES
#include posre_Protein_chain_B.itp
Aside from
Hey James,
I've found the same task of MSU's students :) They simulate membrane
formation without NPT stage ( after NVT they run production MD). From they
reports I've found that simplest membrane system could be formed within
10-30 Ns. But what about try to make such simulation in vacuum at
Hi,
You don't need a .tpr file for removing jumps; a pdb/gro file will do.
Cheers,
Tsjerk
On Oct 24, 2011 2:51 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Steven Neumann wrote: Dear Gmx Users, I am trying to convert my
trajectory using trjconv. ...
trjconv -dump 0
3. Remove jumps if
coordinate file as output can be only trajectory (trr
or xtc file)
4. How to use this frame in:
trjconv -f md2wholeDUMP.xtc -s md2.tpr -pbc nojump -o md2wholeDUMPnojump.xtc
?
Please, help!
Steven
On Mon, Oct 24, 2011 at 2:49 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi, You
a lot.
Regards,
-Vivek Modi
Date: Wed, 19 Oct 2011 13:58:00 +0200
From: Tsjerk Wassenaar tsje...@gmail.com
Subject: Re: [gmx-users] Reference structure for g_covar
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
CABzE1SjU=n78nwo+o0utm7ovdwz4hbgjeylj8x0nbwewwlz
Hi Rui,
In the R terminal ctrl-c cancels the function, not the session.
Cheers,
Tsjerk
On Oct 20, 2011 7:16 PM, Rui Esteves ruimax...@gmail.com wrote:
Hi,
This question seems very basic but I cannot find an answer on google.
I have a R session on a linux command line.
I called a function
Hi Vivek,
I explained related matters in some detail on this list earlier, and
would urge not to use a structure other than the average for
determining the components.
The results on the cosine contents can be illustrated as follows:
I. Using average
Imagine you're moving from place A to place
Hey :)
The reference plays no role in centering. But I guess that Nilesh expects
centering of the solute w.r.t. to the solvent, or is looking at the wrong
center (tric/rect).
Cheers,
Tsjerk
On Oct 17, 2011 7:06 PM, Justin A. Lemkul jalem...@vt.edu wrote:
Nilesh Dhumal wrote: Thanks Justin,
of a snapshot with
no pbc effect, can I use -pbc nojump in trjconv.
nilesh
On Mon, October 17, 2011 1:34 pm, Tsjerk Wassenaar wrote:
Hey :)
The reference plays no role in centering. But I guess that Nilesh expects
centering of the solute w.r.t. to the solvent, or is looking at the
wrong
Yes.
Tsjerk
On Oct 15, 2011 7:21 PM, Yun Shi yunsh...@gmail.com wrote:
Hi all,
I am doing simulations on cluster piece by piece with -maxh and -noappend
options of mdrun.
However, one piece crushed way before approaching the max hours for unknown
reasons. As a result, the part0004.trr file
Selam Ahmet,
I cordially suggest to have a look at
http://catb.org/~esr/faqs/smart-questions.html to phrase your question
more effectively, such that we can provide more tailored help. It
would have been nice to have an example that we could try ourselves.
I find that as preparation for MD
Hi Hualin,
The elastic network should work; the help should be updated...
Note that only the 'elnedyn' method has really been tested.
Cheers,
Tsjerk
On Oct 14, 2011 7:11 PM, Li, Hualin hualin...@uth.tmc.edu wrote:
Hi,Xavier,
Thank you for your reply. The method I used is from previous
Hi Андрей,
That is not possible.
You set a new property on a chempy model instance. load_model converts
that model into an internal representation, simply neglecting the new
property. get_model creates a fresh chempy model instance, which has
no .name property.
If you really, really want to do
Hi George,
You might want to use cmd.get_model() to make your life easier. It turns a
selection into a chempy model, which has an attribute .atom, containing all
the corresponding atoms with names, identifiers, coordinates, etc.
Check scripts on the pymolwiki that do comparable things.
Hope it
believe the file I posted should be
a valid PQR format.
Martin
Am 13.10.11 06:17, schrieb Tsjerk Wassenaar:
Hi Martin,
You can use b and q as selection keywords (help selections):
color red, b 0
color blue, b 0
Or you can use 'spectrum' (help spectrum):
spectrum b, red_white_blue
Hi Martin,
You can use b and q as selection keywords (help selections):
color red, b 0
color blue, b 0
Or you can use 'spectrum' (help spectrum):
spectrum b, red_white_blue
Hope it helps,
Tsjerk
On Oct 13, 2011 12:58 AM, Martin Hediger ma@bluewin.ch wrote:
Dear List
I have the below
Hi Lina,
Not really a Pymol question, is it?
On linux you can use sed:
sed '/^\(ATOM\|HETA\)/s/^\(.\{72\}\)/\1/' filein.pdb fileout.pdb
That means:
/^\(ATOM\|HETA\)/ :: Match lines starting with ATOM or with HETA, and
on those lines execute:
s/^\(.\{72\}\)/\1/ :: Subsitute the
, Thomas Holder
spel...@users.sourceforge.net wrote:
On 10/11/2011 10:16 AM, Tsjerk Wassenaar wrote:
Not really a Pymol question, is it?
well, it's the segment identifier column, so you can do with PyMOL:
set pdb_retain_ids
load input.pdb
alter all, segi=''
save output.pdb
Thanks,
a bit
Hi Valentina,
Check position_restraints (chapter 5).
These are used in standard MD during equilibration, so you can check
any tutorial protocol on how to use them.
Hope it helps,
Tsjekr
On Mon, Oct 10, 2011 at 9:22 AM, auryn_vale...@libero.it
auryn_vale...@libero.it wrote:
Hi to everybody!!!
Hi Gurunath,
Each structure in the NMR ensemble is a fit to the experimental data.
Unlike an MD trajectory, you can not assume that the set of structures
is a proper sample from the Boltzmann distribution, and therefore, the
RMSF can not be expected to correspond to the RMSF of the system. Now,
Hey Justin,
Large RMSD values would indicate non-native structures, which doesn't sound
like what you're looking for. If your goal is simply enhanced sampling, try
REMD.
I think this is put too boldly. There are plenty of examples where
pairs from native ensembles have large RMSD: e.g.,
Hi Liang Liu,
You will never get broader sampling by adding restraints. If you want
to have broader sampling, raise the temperature or add denaturants.
But also ask yourself the question if what you think you want is what
you should be wanting. What is the actual question you're trying to
solve?
Hi Yun,
For comparison, the conditions have to be equal. That does not include
possible hardware issues. So you should be fine.
Cheers,
Tsjerk
On Oct 11, 2011 4:41 AM, Yun Shi yunsh...@gmail.com wrote:
Hi Justin,
I guess you are right, that some processors on that cluster appear to be
much
Hi Lina,
Can you tell more? What version are you using, what system are you on, do
you use a .pymolrc, and what exactly do you do?
Cheers,
Tsjerk
On Oct 9, 2011 5:05 PM, lina lina.lastn...@gmail.com wrote:
On Sun, Oct 9, 2011 at 10:50 PM, lina lina.lastn...@gmail.com wrote:
Hi, I met
10, 2011, at 1:04, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Lina,
Can you tell more? What version are you using, what system are you on, do
you use a .pymolrc, and what exactly do you do?
Version 1.4.
Debian amd64
I did use .pymolrc.
Please kindly notice the problem just recent two
Hi Zhenlong,
I guess that some molecules got split over the boundaries during
equilibration. You have to make them whole before changing the box.
Better to start off with a rhombic dodecahedron though.
Cheers,
Tsjerk
On Thu, Oct 6, 2011 at 6:29 PM, zhenlong li zxl1...@gmail.com wrote:
Dear
I just can't help myself...
(for instance, a rainbow colour scheme based on survey trip?)
Can he do a colour scheme based on LSD trip too?
But it's cool :)
Cheers,
Tsjerk
--
Tsjerk A. Wassenaar, Ph.D.
post-doctoral researcher
Molecular Dynamics Group
* Groningen Institute for
Hey :)
Would g_sgangle be capable of what you want?
Otherwise, your best bet seems to be writing the atoms involved to an
easily readable format (.gro/.pdb) and do the math in Python. I can
send you a backbone Python script for reading .gro/.pdb trajectories
if you want.
Cheers,
Tsjerk
On
Hey :)
If that is what you want, you'll have to turn to programming. But what do
you think to gain from it? First get to the bottom of things you can do with
gromacs already. Then, if the tools available don't help in answering your
question, think of what you'd need to get it done.
Cheers,
801 - 900 of 2217 matches
Mail list logo
