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
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 result in nm. I want
to convert
it to Å. I request you to kindly guide me with the process
Thanking You with Regards.
Arunima Shilpi
Ph. D Research Scholar(Cancer
PM
To: gmx-users@gromacs.org
Subject: [gmx-users] Conversion of nm to Å
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 result in nm. I
want
to convert
it to Å. I request you to kindly guide me
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 dimensions.
It seems that the two tools are quite incompatible, especially when
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
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 trajectory
to be read by MMPBSA.py tool. It
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
Hi gromacs users,
Is there a way to convert gromacs topology format to Amber.
Thanks,
Aiswarya
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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
Hello Everyone,
Any idea how one can convert gromacs trajectory file to amber file. So as to
use the amber tools.
Thank you,
Aiswarya
Sent from my BlackBerry® on Reliance Mobile, India's No. 1 Network. Go for it!--
gmx-users mailing listgmx-users@gromacs.org
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
Thank you Olivier for your response.
SA
--
Message: 2
Date: Thu, 28 Jul 2011 11:20:44 +0100
From: Oliver Grant olivercgr...@gmail.com
Subject: Re: [gmx-users] Conversion of the GLYCAM dihedral parameters
To: Discussion list for GROMACS users gmx-users
-
--
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
: 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:
1311171438.14853.yahoomailclas...@web161422.mail.bf1.yahoo.com
Content-Type: text/plain; charset=utf-8
So my questions
. Once a positive
value is reached, terms for the O2-P-OS-CP potential have been completely
accounted for.
Hope that helps.
Austin-
--- On Tue, 7/19/11, Mark Abraham mark.abra...@anu.edu.au wrote:
From: Mark Abraham mark.abra...@anu.edu.au
Subject: Re: [gmx-users] Conversion of the GLYCAM
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
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) :
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
Dear Oliver Grant
thanks for your attention.
I want to use amber tool for hydrogen bond analysis especially (water
mediated hydrogen bonds and residence time and occupation of them).
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical
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
Dear Oliver
very thanks for your help.
Justin's perl script is good for direct hydrogen bonds, while I want to
study water
mediated hydrogen bonds and residence time and occupation of them.
Are youe sure g_hbond give you residence time of hydrogen bonds?
before you said you used a script to
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
Dear gromacs users
I did simulation of protein-dna by gromacs and amber03 force field. I want
to do some analysis by amber. what is the best way for conversion of gromacs
trajectory and topology files to amber files?
any help will highly appreciated.
--
Leila Karami
Ph.D. student of Physical
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
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 into gromacs format, is it possible?? if so, please let me know
your suggestions.
Thanks,
Ram
--
gmx-users mailing list
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:
I am interested in converting between GROMOS96 bond/angle potentials and
standard
harmonic potentials. The GROMACS manual (version 4) suggests formulae for
doing
so (Eq. 4.38 and Eq. 4.53). However, I am having trouble understanding where
these
come from and find that they seem to give rather
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???
Please help.
See the Web#39;s breaking stories, chosen by people like you. Check out
Yahoo! Buzz.
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
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 I need to convert these
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
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 command for tip5p, the output
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
Hi,
I would like to use nMolDyn for the analysis of the GROMACS trajectories.
I tried VMD and catdcd to convert trr/tpr files to dcd/pdb files. But the
conversion of the dcd/pdb files to nc (netcdf) files using the dcd_to_nc
program of the nMolDyn package does not work. Obviously the header of
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
Thanks in advance.___
gmx-users mailing list
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
Hi everyone
I'd like to convert my Gromacs trajectory to an Amber format for use
with the CAVER program. Reading round, it seems that Amber is
equivalent to the g87 format so I can use trjconv to produce the file.
This all seems to work well (the file gets read in and processed) except
for a
Hi,
I need to convert GROMOS topology file into GROMACS format, I wonder if
someone know of a program in GROMACS or GROMOS packages that does it.
Thanks, Itamar
--
Prediction is very difficult, especially about the future - Niels Bohr
___
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