Hi Ahmet,
That sort of indicates that the file is not there, doesn't it?
Maybe you're not doing what you expect to be doing, or doing it somewhere else.
Cheers,
Tsjerk
2011/1/25 ahmet yıldırım ahmedo...@gmail.com:
Dear users,
g_rms -s em.tpr -f run.xtc
Select group for least squares fit:
Hi Seth,
So you just want to have all unique chain identifiers for the
'polymer' selection? Does the following give what you want?:
polychains = set([i.chain for i in cmd.get_model('polymer')])
Hope it helps,
Tsjerk
On Sun, Jan 23, 2011 at 10:04 AM, Seth Harris set...@gmail.com wrote:
Hi
Oops... That should've been:
polychains = set([i.chain for i in cmd.get_model('polymer').atom])
Sorry for that. :p
Tsjerk
On Sun, Jan 23, 2011 at 10:32 AM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Seth,
So you just want to have all unique chain identifiers for the
'polymer' selection
Hi Joyce,
In pymol use 'set all_states'
Cheers,
Tsjerk
On Jan 22, 2011 8:30 AM, Kwee Hong jestan1...@yahoo.com wrote:
Hi,
I was trying to do some analysis following John's GROMACS tutorial for
solvation study of spider toxin peptide.
I'm using GROMACS-4.5.3 and my command line for g_confrms
You're kidding us! Please stop it, as it draws attention from the questions
that deserve it.
Tsjerk
On Jan 17, 2011 8:27 PM, Nancy nancy5vi...@gmail.com wrote:
Hi All,
For pioglitazone, are the two tautomers depicted in the attached figure the
major forms at pH 7.0?
Also, are there any
Hi Karbalee,
It says : nanometer squared.
Cheers,
Tsjerk
PS. Many of us are not Justin... :p
On Sat, Jan 15, 2011 at 5:33 PM, shahrbanoo karbalaee
shahrba...@gmail.com wrote:
Dear Justin
Hi,I want to use PCA for compare fluctuations two peptides with 13
aa. I use this command g_covar
Hi MKS,
So according to this my minimal box size should be
0.6nm in order to avoid PBS effects and due to the
water effects i have to set it 1nm or higher.
Well, not box size, but the distance from the solute to the box wall :)
So this rule is irrespective of the box type we choose
isnt
Nancy,
Mark already indicated that this is not the proper place to post
questions like that. This forum is about gromacs, not about tautomers,
docking, and certainly not about MarvinSketch.
Cheers,
Tsjerk
On Thu, Jan 13, 2011 at 10:26 PM, Nancy nancy5vi...@gmail.com wrote:
Hi All,
I
This should of course have been sent to the list... Apologies.
Tsjerk
-- Forwarded message --
From: Tsjerk Wassenaar tsje...@gmail.com
Date: Thu, Jan 13, 2011 at 10:47 AM
Subject: all_states failure with 500 or more models
To: Jason Vertrees jason.vertr...@schrodinger.com
Hi
Please let me know what can I do.
thanks in advance
On Thu, Jan 6, 2011 at 11:20 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Mohsen,
I think rotating a molecule with editconf will not rotate the box. Then
again, if it did, it would result in a box violating Gromacs requirements
which connects drug to
a residue inside of hole.
I rotated box with editconf ,solvated system with genbox,neutralized with
genion,
now I want to generate NPT and then generating configuration as umbrella
sampling tutorial.
On Wed, Jan 12, 2011 at 1:53 PM, Tsjerk Wassenaar tsje...@gmail.com
Hi MKS,
The distance between the solute and the sides of the box is separate from
the cutoffs. But, you want to have them large enough to avoid
self-interaction across the PBC. So the distance has to be set larger than
half the size of the cut-off. You probably shouldn't set it lower than 1nm
Hi Joyce,
Can you post the command line? Does it also happen with other force fields?
Is there something notable about the pdb file?
Cheers,
Tsjerk
On Jan 13, 2011 7:48 AM, Kwee Hong jestan1...@yahoo.com wrote:
Hi Mark,
I tried v 4.0.7 and 4.5.1. Both experiencing the same situation.
The
Hey :)
Unfortunately,
trjconv takes a bit of experimenting to get working properly, and there is
no clear how-to to treat the periodicity of any one system.
Sure there is! Just a matter of understanding what you want and
obeying the order:
1. First make your molecules whole if you want them
Hi,
editconf needs to take the masses from a database file if not fed with
a run input file. It will probably miss out on some types of atoms or
get the masses wrong, especially with united atoms and/or dummies.
Probably the density would be correct giving a .tpr file for input.
Cheers,
Tsjerk
Hi Camilo,
The things you desire are in principle possible, but they require code
reorganisation as well as quite a bit of additional coding that isn't
really worth the hassle. Probably it's actually better to split up
trjconv to have one tool for pbc related work and one for fitting
related
Hi Nancy,
This isn't really a Gromacs related question, and it would be better
fit on some chemistry forum. Anyway, whatever answer may come to you,
mind that you're interested in the receptor bound form, which may not
be what you'll find to be the dominant form. It will depend on the
hydrogen
:36 +0100
From: Tsjerk Wassenaar tsje...@gmail.com
Subject: Re: [gmx-users] Re: Average box size
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
aanlktimmyai39nmj6sv008zuuvpt_uhzavhm=tah3...@mail.gmail.com
Content-Type: text/plain; charset=ISO-8859-1
Hi
Hi Mohsen,
I think rotating a molecule with editconf will not rotate the box. Then
again, if it did, it would result in a box violating Gromacs requirements.
Either way, it's not going to work like that. Build a new box after
rotation... And have a good look at what you're actually trying now by
PM, Navjeet Ahalawat navjeet0...@gmail.com wrote:
Hi Tsjerk,
Thanks for reply, Please can you tell me how can I get the average box
length (a b c) of my triclinic box for my next step.
Message: 2
Date: Mon, 3 Jan 2011 18:17:15 +0100
From: Tsjerk Wassenaar tsje...@gmail.com
Subject: Re: [gmx
.
Message: 4
Date: Tue, 4 Jan 2011 12:35:36 +0100
From: Tsjerk Wassenaar tsje...@gmail.com
Subject: Re: [gmx-users] Re: Average box size
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID:
aanlktimmyai39nmj6sv008zuuvpt_uhzavhm=tah3...@mail.gmail.com
Content-Type
Hey Leila,
Why all the fuzz? You can do this with trjconv using an index file.
The following oneliner (:$) should write you the index file you need.
python -c
'r,a,b,c=range,1868,24086,24100;open(r.ndx,w).write([x]\n+\n.join([str(i)
for i in r(1,a)+r(b,c)+r(a,b)]))'
Hope it helps,
Tsjerk
On
Hi Navjeet,
The box is defined as a triangular matrix, so the volume equals the product
of the diagonal elements.
Hope it helps,
Tsjerk
On Jan 3, 2011 5:57 PM, Navjeet Ahalawat navjeet0...@gmail.com wrote:
Hi all
I did NPT simulation for 30 ns using triclinic box (-angles 88.30,
107.40,
Hi Leila,
r.ndx would be the index file indeed. Sorry for not explicitly mentioning
that. For the rest, the most important question is 'did it work?' Knowing
python is not so important, unless you're determined to understand how it
works :) As for the numbers, python always goes up to, not
Hi Jason,
It appears that Pymol segfaults rendering when a cgo object spans
multiple states, and all_states is set on:
from pymol import cmd
set all_states,1
cmd.load_cgo([COLOR,1,1,0,SPHERE,3,0,0,1],name=bla,state=2)
cmd.load_cgo([COLOR,1,0,0,SPHERE,0,0,0,2],name=bla,state=3)
ray
This
Hey :)
A little while ago I tried growing in molecules in a solution starting from
shrunken coordinates. It would have been very useful if the box also had
taken part in the energy minimization... That would have saved quite bit of
trouble relaxing with NPT MD.
Just my two cents :)
Tsjerk
On
Hi Erik,
Happy New Year!
Last year (:p) I rewrote the routine from Andrea Amadei for
application of rotational constraints in a statistical mechanical
consistent manner. It's completely parallellelellized and consistent
with pd/dd as well as application every so many steps. The tests seem
good,
Hi Mohsen,
I think you'll have to get a bit creative with g_traj to get the COMs,
followed by either some simple scripting or nifty usage of paste and awk
(something like: paste com1.xvg com2.xvg | awk '/^...@#;]/{print $2-$6,
$3-$7, $4-$8}').
Hope it helps,
Tsjerk
On Dec 25, 2010 2:40 PM,
Hi Hassan,
It seems the scripting language of the Gimp has changed a bit since
the version I used at the time of writing that script. The Gimp is
also only used for conversion of the xpm to png, which it did better
than convert. The important parts for recoloring are the lines using
convert,
Ni Hao Cun Zhang
The real 'problem' is that Pymol does not allow selection based on
coordinates. Probably this should be on the wish list (and easy to
implement). Expressions are allowed, for instance selecting based on
b-factor or occupancy.
In your script, you can use some shortcuts. Maybe
Hi Pawan,
I can add two things. First of all, the score is simply the projection
of a point (conformation) onto the eigenvector. Second, extreme
scores/projections, be it positive or negative, are usually most
unlikely, thus corresponding to highest energy. For the lowest
energies, you'd be
Hi Pawan,
No, there are scores and times, no energies.
Cheers,
Tsjerk
On Fri, Dec 10, 2010 at 6:39 AM, pawan raghav pwnr...@gmail.com wrote:
Dear justin,
Thanks for your useful suggestions but not the right way to post these
things. Anyway Dear I have already read the link mentioned by you
Hi Ahmet,
I'm not sure whether it's been checked. It has been found that NMR
structures tend to yield larger deviations than crystal structures. If
you're going to try, due make sure to compensate for other potential
influences, such as the size and sphericity of the proteins.
Cheers,
Tsjerk
Hey,
For this particular conversion you can also usually use 'mv':
mv file.pqr file.pdb
Btw, many of these file types are human readable. It usually helps quite a
bit to look at the files and get acquainted with the file formats.
Cheers,
Tsjerk
On Nov 22, 2010 12:42 PM, Mark Abraham
Hi Ithayaraja,
That's not an error in pdb2gmx. It's an error in your input file. One
of your residues (H341) is not complete. This is the first thing to
check when going for a simulation. You'll have model the missing atoms
in before you can proceed.
Cheers,
Tsjerk
On Wed, Nov 24, 2010 at 5:09
Hi,
Visualization software can sometimes assign the secondary structure
incorrectly.
There has been an interesting discussion on this on the Pymol user
list years ago
(http://www.mail-archive.com/pymol-us...@lists.sourceforge.net/msg01574.html).
Secondary structure assignment is foremost
Hi Vignesh,
If your covariances show different ranges, isn't that a difference
between your systems, wild-type and mutated? Then again, there's also
noise in the covariances (noise in the fluctuations, ergo noise in the
noise ;)). The rest might be comparable, making scaling based on the
extremes
...@itqb.unl.pt wrote:
Hello,
No, the hole don't correspond to parts of the protein sticking out on the
other side. The protein is in the center of the box and the holes are not
due to pbc issues.
Diana
On Fri, Nov 5, 2010 at 10:10 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hey, Do
the box doesn't have the right shape and of pbc issues, but it seems to me
that the holes are present in this box, i.e. I don't think they are an
artifact of trjconv.
Thanks for the help
Diana
On Sat, Nov 6, 2010 at 8:08 PM, Tsjerk Wassenaar tsje...@gmail.com wrote:
Hi Diana, Yeah...
--
gmx-users
Hey,
Do the holes match the parts of the protein sticking out on the other side?
Tsjerk
On Nov 5, 2010 8:14 PM, Vitaly Chaban vvcha...@gmail.com wrote:
On Fri, Nov 5, 2010 at 3:03 PM, vedat durmaz vedat.dur...@gmx.net wrote:
hi vitaly,
the only acetonitrile boxe that i was able to find is
Hi :)
I suspect the volume fluctuations are not symmetric around the
idealized volume at 1 bar. I think that would mean that the average
volume does not correspond to the idealized volume, as you assumed.
Cheers,
Tsjerk
On Wed, Nov 3, 2010 at 12:19 AM, Dallas Warren dallas.war...@monash.edu
Hi Mustafa,
Check the section on periodic boundary conditions in the manual. Also
be sure to use 'show cell' in Pymol to display the triclinic unit
cell. That will show you the differences. Besides that, do a direct
comparison of the lines encoding the boxes; either the last line of a
.gro fil,
Hi Lin,
Not really surprising that water, even SPC, evaporates at 498K and 1 bar,
right? (Assuming you performed the simulation at 1 bar). The expansion of
the system with NVT seems unlikely, as the volume is fixed. If it really
expands, you have pressure coupling turned on, and should double
atom has which index. Thats why i was hoping to find a way to get the
'linenumber-dependent' index of an atom.
Thanks for your help so far.
Martin
On 31.10.10 18:31, Tsjerk Wassenaar wrote:
Hi Martin,
So it seems I was right :D
ID is an atomic property, read from the PDB file, whereas
Hey,
There's quite a number of people that should be rereading their statistics... :p
First of all, there are instantaneous measurements, averages and
fluctuations. If the statistics (mean/fluctuation) are 7 +/- 500, then
that doesn't mean that the average of 7 is an estimate that may be off
by
Hi Martin,
So it seems I was right :D
ID is an atomic property, read from the PDB file, whereas index is an
'internal' identifier. Following Jasons comments, ID is not changed upon
additions/deletions, whereas index does.
For your purpose, you probably want to make sure that the IDs are
your questions.
Cheers,
Tsjerk
-- Forwarded message --
From: Chih-Ying Lin chihying2...@gmail.com
Date: Thu, Oct 28, 2010 at 8:28 AM
Subject: RMSF = still confused ?
To: Tsjerk Wassenaar tsje...@gmail.com
Hi Tsjerk:
Well i am still confused about the RMSF.
1. Consider
Hi,
The tutorial states that the quality needs to be increased prior to
ray-tracing. But it seems to me that the {sphere,stick}_quality
settings apply to the OpenGL rendering, whereas the raytracer uses
'real' spheres and cylinders. Even when setting sphere_quality to 0,
'ray' will still give
Hi Leila,
Maybe you're better off trying:
1. trjconv -pbc nojump # choose system for output
2. trjconv -center -pbc mol # choose protein/dna for centering, system
for output
Centering is done before removing PBC, so you should be safe with two passes.
You might also want to play with -ur
Hi Leila,
2.xtc should contain all that you want.
My point was that you shouldn't need to separate protein/dna and
solvent into two trajectories to be combined later.
Note that this only concerns visualization. You can do distance and
H-bond calculations on the original trajectory, as the
Right :)
On Wed, Oct 27, 2010 at 2:27 PM, leila karami karami.lei...@gmail.com wrote:
Dear Tsjerk
Thus, as you said, Xtc file obtained from trjconv –pbc nojump only concerns
visualization. Thus, can I use old xtc file (with out –pbc nojump) for
analysis such as interfacial waters and water
Hi,
Lin, please think your questions over thoroughly in stead of flushing
every thought right to the mailing list. It also helps to stick to a
certain subject (reply) to make sure everything ends up in the same
thread. Maybe it's not a bad idea to read over
editconf -scale -1 -1 -1
On Tue, Oct 26, 2010 at 12:56 PM, Erik Marklund er...@xray.bmc.uu.se wrote:
#ZHAO LINA# skrev 2010-10-26 11.46:
Hi,
which can help to get the mirror reflection of a known protein?
Thanks,
lina
If it's just one conformation, then I'd just write a script that
Hi Lin,
How many residues do you have and how many points do you get? (Only answer
for yourself). We're no substitute for your brain, you know...
Cheers,
Tsjerk
On Oct 25, 2010 7:47 AM, Chih-Ying Lin chihying2...@gmail.com wrote:
Hi
g_rmsf -f abc.xtc -s abc.tpr -res -o abcrmsf.xvg
Hi,
You're not
seeing complete mixing of your two species, but there is some diffusion
between the phases, otherwise both of your particles should drop to exactly
zero density on either side of the box middle, wouldn't they?
No, not if there are undulations of the interface.
Cheers,
Tsjerk
...
-- Forwarded message --
From: Tsjerk Wassenaar tsje...@gmail.com
Date: Mon, Oct 25, 2010 at 12:39 PM
Subject: Re: [PyMOL] Question about Iterate and Edit-Mode
To: Martin Hediger ma@bluewin.ch
Hi Martin,
Without diving into the source, I think it is more like:
for i
Never get used to that only-reply-to-sender policy...
-- Forwarded message --
From: Tsjerk Wassenaar tsje...@gmail.com
Date: Mon, Oct 25, 2010 at 12:30 PM
Subject: Re: [PyMOL] What is the difference between Atom ID and Index
To: Martin Hediger ma@bluewin.ch
Hi Martin,
ID
Hey Lin,
Did you consider PBC?
Also, I wouldn't include the bromide if I were you, as it just adds noise,
because it can move around freely. You seem to be interested in the change
in dipole moment in the cation only, anyway.
Cheers,
Tsjerk
On Oct 21, 2010 7:02 AM, Chih-Ying Lin
Hi Rama,
You can convert the .trr file to readable .gro/.g96 with trjconv.
Frames with positive times will correspond to eigenvectors; the time
indicates the eigenvector index. Make sure not to use any options like
pbc/fitting :p
Cheers,
Tsjerk
On Sat, Oct 16, 2010 at 7:00 AM, Ramachandran G
Hi,
Do mind that calcium binding may involve (quantum) effects that are ill
captured by classical force fields. If the binding site plays a central role
in your research question, this may be problematic.
Cheers,
Tsjerk
On Oct 16, 2010 2:34 PM, Justin A. Lemkul jalem...@vt.edu wrote:
leila
Hey Floris,
Here's a python script to write out the last frame from a .trr file:
#PYTHON
#!/usr/bin/env python
import sys
# Read a 32 bit unsigned int
def i(x): return sum([ord(x[j])(24-j*8) for j in range(4)])
# Open the file, find the end and go back
f = open(sys.argv[1],'rb')
f.seek(0,2)
Hi Anupam,
I recently wrote a small python script to convert gromacs .xpm files
to numbers. Maybe it'll be of some use to you:
Cheers,
Tsjerk
###
#!/usr/bin/env python
import sys
def unquote(s):
return s[1+s.find(''):s.rfind('')]
def uncomment(s):
return
Hi Sonali,
First of all, you'll have to find a force field that supports tyrosinate and
serinate. These aren't generally considered titratable and are consequently
not in the list for interactive selections with pdb2gmx. Once you've found a
suitable force field, you'll have to set the protonation
Hi Stefano,
Using C N CA CD instead of C CA N C inverts the improper dihedral. And
unlike all atom force fields, you can start from an L-proline :)
Cheers,
Tsjerk
On Sep 24, 2010 10:46 AM, Stefano Pieraccini stefano.pieracc...@unimi.it
wrote:
Dear Gromacs users,
I would like to use
Hi Ramiro,
Assuming your rings are nicely planar, and representing the ring as:
1-2-3
| |
6-5-4
you can get the plane normal vector as the vector cross product from
(3)-(1) and (5)-(1).
Doing so for both rings gives you the two normal vectors. The angle
then follows from the dot product of
(cpv.get_angle(dir1, dir2))
python end
Cheers,
Thomas
On Thu, 2010-09-23 at 13:02 +0200, Tsjerk Wassenaar wrote:
Hi Ramiro,
A bit of linear algebra wouldn't hurt... :p
In python:
def vsub(a,b): return a[0]-b[0], a[1]-b[1], a[2]-b[2]
def dot(a,b): return a[0]*b[0]+a[1]*b[1]+a[2]*b[2]
def svmul(s
Probably I wasn't the only one who got this in a personal mail box,
but I'll forward it anyway. And, no, I'm not a private tutor, unless
I've explicitly indicated otherwise.
Tsjerk
-- Forwarded message --
From: AJANI HARESH ajani_har...@yahoo.co.in
Date: Thu, Sep 16, 2010 at
Hi Renuka,
Are you sure that's what you want? It will read something like:
for i in __import__(glob).glob(cluster_*.sdf): cmd.load(i)
But I think it's more elegant to use two commands for this... :-P
import glob
for i in glob.glob(cluster_*.sdf): cmd.load(i)
May seem like a small difference,
Hi,
One work-around for the -chainsep situation you've observed is to remove or
rename the terminal oxygen atoms (OXT) that pdb2gmx is complaining about when
it tries to merge the chains. It should be taking care of that itself, but
handling it yourself might help. pdb2gmx can probably
, 9/7/10, Tsjerk Wassenaar tsje...@gmail.com* wrote:
From: Tsjerk Wassenaar tsje...@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, 11:14 AM
Hi,
One work-around for the -chainsep
Hey,
It might also be related to the PBC, with gromacs not writing whole
molecules anymore. Maybe a link to a picture would be good, showing
protein beads spheres, together with the (triclinic) unit cell.
Cheers,
Tsjerk
On Mon, Sep 6, 2010 at 12:05 PM, XAvier Periole x.peri...@rug.nl wrote:
Hi Prabha,
Why did you choose that force field, and what CA atom type?
Tsjerk
On Thu, Sep 2, 2010 at 1:30 PM, praba vathy sumipraba2...@gmail.com wrote:
Dear Sir,
We have chosen force field Gromos96 53A6 parameter set.
In that forcefield, how we add this CA atom type.
Prabha
--
Hi Chih-Ying Lin,
There's no such thing as a pi bond in a classical force field, bonds
are merely connections with a certain distance based potential.
Gromacs doesn't deal with polarity, the distribution of charges, etc.
is part of the force field. Better check the papers relating to the
force
Hi Sebastien,
If you have multiple poses of the same molecule in your sdf file, you
can translate them into a multi-model PDB file, writing the score and
rmsd values to the bfactor and occupancy field. This you can then load
into pymol, allowing you to step through the poses. With the command
Pawan,
What are you trying to do?
Tsjerk
On Fri, Aug 27, 2010 at 9:16 AM, pawan raghav pwnr...@gmail.com wrote:
I am posting this question second time so please tell me, where I was wrong?
In manual g_analyze reads an ascii file and analyzes data sets, in which
input file was graph.xvg. To
Hi Pawan,
These are the maximum and minimum projections on the eigenvectors. They are
very unlikely to correspond to energy minima, as minima will be modal. Think
of a pendulum, projecting the position on the floor. The extreme projections
actually correspond to states of higher (potential)
Hi,
the interface is now A + B - AB
WHy not HALF of (A+B-AB) ?
You are right.
A + B - AB gives the Buried Surface Area, which is the amount of
surface that gets excluded from the solvent by complexation (and
consequently is twice the size of the interface).
:)
Tsjerk
--
Tsjerk A.
Hey,
directly. I think you want this (assuming that cols 5,6,7 give you the
dx,dy,dz, which I believe that they do):
cat pullx.xvg | grep -v '[#|@]' | awk '{print $1,sqrt($5*$5+$6*$6+$7*$7)}'
my.data
Nothing directly harmful of course, but why using three programs for
this? awk will do
Hi Pawan,
This goes beyond a few lines of explanation. Move away from the tools
g_covar and g_anaeig slowly ;) and do some more background reading on
principal component analysis. I've tried to explain it in my tutorial
at http://nmr.chem.uu.nl/~tsjerk/course/molmod/analysis1.html (which
will
Hi Sdat5885,
Have you started a fresh session, or did you a. load a session file or
b. did some other things you didn't mention before? It may be that you
have specifically set the highlight color for your protein. The
default is not grey, but whatever color the C alpha atom has. You
might want
Hi Udi,
Square the numbers... It's Root Mean Square Deviation, right? But roots
don't add up like that.
Cheers,
Tsjerk
On Aug 12, 2010 12:02 AM, udi udi_...@012.net.il wrote:
Hi gromacs users,
I’m simulating a protein that consists of 5 domains. I have calculated the
whole protein’s
Hi Greg,
So you want a distribution of MSD, right?
I have trajectories which has been obtained from simulating 20,000 atoms in
NVT simulation for 25ns. I recorded the trajectory every 3ps which means
that I have 60,000 data points per atom.
25000/3 = 8333
Where do these 60k per atom come
Hi Pooja,
Try to get a grip on the file types and what they contain. A .cpt file
is a checkpoint file containing a single configuration. Not much
fluctuation to expect there. This sort of analysis only makes sense
for a trajectory, or at least an ensemble of structures. Try the .xtc
or the .trr
Sonali,
Why wouldn't it be correct if you did just what David told you to do? And
how would you be able to check yourself whether you were correct? We can't
hold your hand here for every step you make. Have you already gone through
the tutorial material linked on the Gromacs website? If not,
Hi Vivek,
Your workflow sort of reminds me of http://xkcd.com/763/ :)
First of all, make sure that you find a way with a minimal number of
operations. Every time you do something, you may negatively influence
the image quality. Also make sure to always use PNG format for
intermediate stages,
Hi,
The parameters for ATP (and several other building blocks and
molecules) in the GROMOS 53a5 and 53a6 force fields are, AFAIK,
inherited from the older versions, albeit with some modifications to
bring them in line with the rest of the force field. So they weren't
reparameterized and thus do
Hi Prija,
You can do it with a bit of Python
ss = [ i.ss for i in cmd.get_model(n. ca).atom ]
print Helix content: %5.2f%% % (100.0*ss.count(H)/len(ss))
print Sheet content: %5.2f%% % (100.0*ss.count(S)/len(ss))
The first line gets a list of the secondary structure flags of the
selection n. ca.
Hi Chris,
That was indeed what happened with the first version. The '$q' bails out at
the last line without editing.
Of course it's also easy to write a python script doing it, combined with
find -exec.
Cheers,
Tsjerk
On Jul 5, 2010 11:57 PM, Chris Neale chris.ne...@utoronto.ca wrote:
Shay:
Hi Chris,
What about:
find . -name *.gro -exec sed -i -e '$q' -e '3,$s/^\(.\{44\}.\).*$/\1/' {} \;
Assuming using a format %8.3f for coordinates and a single frame in
the .gro file. Otherwise things will get more complicated.
Cheers,
Tsjerk
On Sun, Jul 4, 2010 at 12:45 AM,
Hi Stephan,
snip
I did this from the biggening, it's strait forward as you said. The problems
with the tutorials is they already work, and are missing a shlew of problems
one may incounter when doing more complicated things, etc...
It must have been a disappointment while going for your
Hi,
ATOM 12 CA SER 2 23.444 51.157 35.390 1.00257.41
The last column is the occupancy (1.00) and temperature factor numbers
concatenated. You can fix the symptoms by editing the file by hand so that
these numbers occupy the right columns - see the PDB format.
This illustrates buggy
Hi,
Okay, maybe I should delve into the code for this, but I (and probably
Joao too) was wondering how (if) Pymol determines the valence of a
bond. I.e. can Pymol distinguish between ethane, ethene, and ethyne?
Cheers,
Tsjerk
On Thu, Jul 1, 2010 at 5:58 PM, João Rodrigues anar...@gmail.com
Hi Hassan,
If you have an index file with all the groups, you can use something like:
#!/bin/bash
groups=`grep ^\[ index.ndx | wc -l`
for ((i=0; i$groups; i++))
do
echo $((i++)) $i | g_dist ...
done
This will take groups 0 and 1, 2 and 3, etc, passing the selections to
g_dist. If you want
Hi,
In the mathematical sense, gromacs will only use the frames in the
trajectory for which time modulus dt equals 0 (time % dt == 0).
Cheers,
Tsjerk
On Wed, Jun 30, 2010 at 11:47 AM, XAvier Periole x.peri...@rug.nl wrote:
-dt will define the frequency of analysis that a program will do.
In
Hi Shahab,
I used [ g_rama -f *.xtc -s *.tpr -o rama.xvg ] command for analysis of
Was that your actual command line? If you used a .tpr, why didn't it
have all the dihedrals defined then? How did you get it? Anyway, you
should be able to assert that the dihedrals mentioned are in fact your
Hi,
Not necessary!
If the dimer separates across the boundaries you have
a problem of fitting the two together while they are separated.
This is only if you use the dimer. The monomers would be fine.
That was the case before gromacs 4. But the current versions don't
keep molecules whole.
Hi Shahab,
The dihedral definitions should be in the .top file. But you don't
give any clue to what you've done or what you're doing, so there's
nothing more for us to say to try and help you.
ok. [ g_rama -f *.xtc -s *.tpr -o rama.xvg ] is my actual command line.
So you're actually using
Hi Nayef,
grompp –f em.mdp –c fws_b4em.gro –p fws.top –o fws_em.tpr
genion –s fws_em.tpr –o fws_ion.gro –nname CL- –nn 2 –g fws_ion.log
[select Group 12: SOL]
pico fws.top [reduce number of SOL by two and add 2 CL- at the end of the
file]
This is all fine. You take the structure before em,
Hi Kun,
Can you tell more about what you are doing? What are you analyzing?
How large is the system? Which groups do you use for analysis. Etc.,
etc. Now, you might be right, but you might as well be jumping to
conclusions.
Cheers,
Tsjerk
On Tue, Jun 29, 2010 at 4:12 PM, Kun Huang
Hi Chris, Carla,
Sorry I didn't reply before. To understand the projections, first
consider the following. Take a single atom with three coordinates
(x,y,z). These coordinates are the projections onto a set of (three,
Cartesian) axes. If you consider, e.g., the projection of the
coordinates onto
1101 - 1200 of 2217 matches
Mail list logo
