OP, I give you 10/10. First time I laugh out loud reading the GMX mailing
list.
/J
On Wed, Aug 21, 2013 at 5:05 AM, Arunima Shilpi writetoas...@gmail.comwrote:
Dear Sir
I have to query as to how do we convert the paramaters in nm to Å
--. For example the RMSD and RMSF calculation gives
First port of call for a question like this should be a search engine
http://en.wikipedia.org/wiki/Angstrom
Catch ya,
Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical Sciences, Monash University
381 Royal Parade, Parkville VIC 3052
dallas.war...@monash.edu
+61 3
probably you can try catdcd
On 01/21/2013 11:29 AM, Anna Marabotti wrote:
Dear gmx-users,
I followed the suggestions by Justin and Daniel to convert the
trajectories, but still Amber does not recognize the correct format
and complains about the fact that it does not find the correct box
On 1/17/13 6:22 AM, Anna Marabotti wrote:
Dear all,
we'd need to convert a trajectory in .xtc format (and the related topology file)
to a format that could be read by Amber program (I'd need to perform MM-PBSA
calculations).
We tried to do it using VMD, but failed to produce a correct
On Jan 17, 2013, at 12:27 , Justin Lemkul wrote:
On 1/17/13 6:22 AM, Anna Marabotti wrote:
Dear all,
we'd need to convert a trajectory in .xtc format (and the related topology
file)
to a format that could be read by Amber program (I'd need to perform MM-PBSA
calculations).
We tried
On 8/09/2011 6:06 PM, aiswarya pawar wrote:
Hi gromacs users,
Is there a way to convert gromacs topology format to Amber.
Did you try Googling for such a tool first? :) There probably isn't one,
because starting from scratch with leap is sufficiently easy that a
conversion tool is not worth
aiswarya.pa...@gmail.com wrote:
Hello Everyone,
Any idea how one can convert gromacs trajectory file to amber file. So as to
use the amber tools.
The key is finding a compatible intermediate that can be converted. I've found
that PDB format is pretty universal. I have a script that
Hi Justin,
Thank for the quick response. I would try out your script for the conversion.
Best,
Aiswarya
--Original Message--
From: Justin A. Lemkul
To: Aiswarya Pawar
To: Discussion list for GROMACS users
ReplyTo: jalem...@vt.edu
Subject: Re: [gmx-users] Conversion of gromacs trajectory
-
--
Message: 4
Date: Wed, 20 Jul 2011 07:17:18 -0700 (PDT)
From: Austin B. Yongye ybau...@yahoo.com
Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters
in the GROMACS format.
To: Discussion list for GROMACS users gmx-users@gromacs.org
Message-ID
are always set to 0 and the barrier heights have sometime a negative
value.
Thank you again for your advice.
SA-
Message: 1
Date: Tue, 19 Jul 2011 11:08:55 -0700 (PDT)
From: Austin B. Yongye ybau...@yahoo.com
Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters
, 19 Jul 2011 11:08:55 -0700 (PDT)
From: Austin B. Yongye ybau...@yahoo.com
mailto:ybau...@yahoo.com
Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters
in the GROMACS format.
To: Discussion list for GROMACS users gmx-users@gromacs.org
mailto:gmx-users
On 19/07/2011 11:56 PM, sa wrote:
Dear GROMCS users,
I am trying to convert some GLYCAM parameters in GROMACS format. For
this purpose, I am using the latest GLYCAM parameters downloaded from
the RJ. Woods' website and the examples given in the acpype code (here
for the dihedral angles) :
...@anu.edu.au
Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters in the
GROMACS format.
To: Discussion list for GROMACS users gmx-users@gromacs.org
Date: Tuesday, July 19, 2011, 7:08 AM
On 19/07/2011 11:56 PM, sa wrote
I suppose it depends on what kind of analysis you would like to do... I'm
not aware of any scripts for converting back from gmx into amber
trajectories but I have done this before when doing an mmpbsa calculation
using ambertools. As I only needed snaphots of the trajectory and not
energies or
Hi Leila,
I've done this with g_hbond and g_bond. If you search the forums there is a
perl script available from Justin Lemakul that will do this for you. You can
do it manually too if you have only a few to look at. Its a little tricky
but a lot easier than traj conversion. :) I was able to get
You can try using vmd. It has a powerful language selection and it can
be used remotely.
There is one disadvantage: the trajectory MUST fit into memory since vmd
loads the trajectory into memory.
If this is not the case, you can use the script bigdcd that permits
to load one frame in memory,
Hi Leila,
I would try the other suggested options like catdcd or vmd. The script is a
pain and you would have to adapt it to work with DNA. It cost me a lot of
time.
I used g_hbond for residence time like this:
g_hbond -f 8_fullMD_CA.xtc -s 7_fullMD.tpr -n g_hbond.ndx -a 170 -num
g_hbond.log
Really? This is really great!
Is there any need to specify the location of the vmd libraries?
If a tpr file is needed for the analysis (eg: trjconv -pbc mol) is this
somehow still possible?
On Apr 16, 2010, at 10:07 PM, Roland Schulz wrote:
In case you use the GIT version of the analysis
On Sat, Apr 17, 2010 at 7:54 AM, XAvier Periole x.peri...@rug.nl wrote:
Really? This is really great!
Is there any need to specify the location of the vmd libraries?
By default it tries to find them at
/usr/local/lib/vmd/plugins/*/molfile
If you have them installed somewhere else you can
VMD reads Desmond trajectories and writes GMX format ...
Rests the topology to deal with ...
On Apr 16, 2010, at 4:15 PM, ram bio wrote:
Dear All,
I have run a dynamics of protein ligand complex in lipid bilayer dppc
using desmond software and would like to convert the trajectory files
files
Thanks Xavier,
Could you make it more eloborate...
Ram
On Fri, Apr 16, 2010 at 4:38 PM, XAvier Periole x.peri...@rug.nl wrote:
VMD reads Desmond trajectories and writes GMX format ...
Rests the topology to deal with ...
On Apr 16, 2010, at 4:15 PM, ram bio wrote:
Dear All,
I have run a
Well I guess you want to use gmx analysis tools so you'll have to
build the gmx topology of your system when necessary! Often
only a pdb file or a gro file is sufficient.
On Apr 16, 2010, at 5:24 PM, ram bio wrote:
Thanks Xavier,
Could you make it more eloborate...
Ram
On Fri, Apr 16, 2010
In case you use the GIT version of the analysis tools you don't need to
convert the trajectories first.
I've added that the analysis tools can read all vmd supported file formats
if GROMACS finds the vmd libraries.
Roland
On Fri, Apr 16, 2010 at 11:33 AM, XAvier Periole x.peri...@rug.nl wrote:
P.R.Anand Narayanan wrote:
Dear gromacs users,
How can I convert a certain concentration of a compound (say in mg/ml)
to be used in my simulations, into number of molecules to be added in
the system???
Basic general chemistry: from mg/mL to molarity, then to number of molecules per
unit
Jennifer Williams wrote:
hello gromacs users,
I am working with a silica structure which is parallepiped in structure,
i.e the unit cell is
46.4207 37.7846 18.9596 angles =90, 90, 120
I have a structure file in .xyz and .pdb but the units are in Angstroms
and for gromacs I assume that
2009/6/5 Dmitri Dubov ddu...@ngs.ru
Hi, all
Using gromacs 3.3 I try to work with tip5 water, but I fail to convert
water molecules of gro-file to tip5 kind. Conversion to tip4p from spc is
easy with pdb2gmx
pdb2gmx -f my_spc.gro -water tip4p -o my_tip4.gro -p my_tip4.top
Does it really
Dmitri Dubov wrote:
Hi, all
Using gromacs 3.3 I try to work with tip5 water, but I fail to convert
water molecules of gro-file to tip5 kind. Conversion to tip4p from spc
is easy with pdb2gmx
pdb2gmx -f my_spc.gro -water tip4p -o my_tip4.gro -p my_tip4.top
, but when I apply similar
I don't know about netcdf, but you can use wordom to convert from xtc to
dcd.
Contact me off list if you don't succeed - I'm not sure whether the
online documentation of wordom is up-to-date.
Ran.
Tobias Unruh wrote:
Hi,
I would like to use nMolDyn for the analysis of the GROMACS
minnale wrote:
Hi all,
I am interested about analyse some of the results with amber and
gromacs md packages. Could anyone tell me how to convert .xtc of gromacs
to trajectory input for amber.
eagerly waiting for reply
The *exact* same question was asked yesterday:
thanks alot Justin for your reply
On Tue, 09 Sep 2008 Justin A.Lemkul wrote :
minnale wrote:
Hi all,
I am interested about analyse some of the results with amber and gromacs
md packages. Could anyone tell me how to convert .xtc of gromacs to
trajectory input for amber.
eagerly
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