hello gromacs
i an working on protein ligand complex with lipid membrane (popc)
grompp -f minim.mdp -c popc128.gro -p topol_popc.top -o em.tpr -maxwarn -1
after this fatal error atomtypes CA not found
and only md.oonly mdout is formed
kindly help
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Hi,
I have a problem with that the order of atoms in my topology does not match the
order of atoms in the gro-file. I use amber99sb and I have built itp-files on
my own for the molecules that are not present in the library. Each IMI
contains 9 atoms and each SOL 3 atoms and the ZN is one atom
Hi Rinu,
See what forcefield files you include in your topology, then go to the force
field folders and check if those indeed have that atom types.
You must indeed be missing the CA type. Likely, you just forgot to include some
topology file.
V
On 2 Jul 2014, at 10:23,
Hi,
trjconv is a very versatile tool.
if you do trjconv -h it will tell you:
Option -center centers the system in the box. The user can select the group
which is used to determine the geometrical center. Option -boxcenter sets the
location of the center of the box for options -pbc and -center.
Hello dear gmx-users,
I tried to restart the calculation, but there is always one checksum error as:
Program mdrun_mpi, VERSION 4.6.1
Source code file: /home/kit/ipc/nw2011/gromacs-4.6.1/src/gmxlib/checkpoint.c,
line: 2155
Fatal error:
Checksum wrong for 'pull.xvg'. The file has been replaced
On 7/1/14, 11:28 PM, Chetan Mahajan wrote:
Thanks, Justin. *Until now, I was thinking that xtc coordinates are
wrapped. It's good to know that coordinates from xtc files are unwrapped
(please comment if not correct, since we talked only with respect to gro
That is correct. mdrun doesn't
On 7/2/14, 12:02 AM, shivangi nangia wrote:
Hello gmx-users,
This is regarding inserting required number of TIP3P water molecules using
genbox.
I have a system containing POPC, peptide, water molecules ions.
For some system set up, I had to delete all the waters and ions ( The box
size was
On 7/2/14, 12:27 AM, Andy Chao wrote:
Dear GROMACS Users:
I would like to convert a GRO file to the TOP file. Is it a better way to
use
pdb2gmx -f device.gro -p device.top
or to use
g_x2top -f device.gro -ff oplsaa -o device.top?
That depends. If the contents of device.gro consist of a
On 7/2/14, 6:07 AM, RINU KHATTRI wrote:
hello gromacs users
i used 43a1 force field(Gromacs 4.5.7) in the atomtype.atp file in the
place of CA CA2+ is present in ffnonbonded.itp file CA and CA2+ both are
present according to tutorial i have been followed all the step
still em.tpr not formed
On 7/2/14, 5:59 AM, Guo, Yanan (IPC) wrote:
Hello dear gmx-users,
I tried to restart the calculation, but there is always one checksum error as:
Program mdrun_mpi, VERSION 4.6.1
Source code file: /home/kit/ipc/nw2011/gromacs-4.6.1/src/gmxlib/checkpoint.c,
line: 2155
Fatal error:
Checksum
On 7/2/14, 3:31 AM, Emma Ahlstrand wrote:
Hi,
I have a problem with that the order of atoms in my topology does not match the order of
atoms in the gro-file. I use amber99sb and I have built itp-files on my own for the
molecules that are not present in the library. Each IMI contains 9 atoms
Hello,
in short : it is possible ? I use the gromacs v4.6.5.
Thanks
Stéphane
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On 02 Jul 2014, at 12:55, ABEL Stephane 175950 stephane.a...@cea.fr wrote:
Hello,
in short : it is possible ? I use the gromacs v4.6.5.
No.
Carsten
Thanks
Stéphane
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On 7/2/14, 4:40 AM, Dawid das wrote:
I have managed to deal with this problem in following way:
In topology file some bonding parameters were actually missing but some
bonding parameters were not needed, e.g. U-B or dihedral parameters for
atoms which are not connected, that is they belong to
On 7/2/14, 5:39 AM, Linlin Sun wrote:
Hello everyone,
In order to build a virtual site which is independent from other structure,
I have created a new atom type and set the mass of this new atom type to
zero. However, when I use* grompp*, it failed with fatal errors, which
complain about the
Thanks for your quick and also fast (;)) reply, Carsten.
Stéphane
--
Message: 4
Date: Wed, 2 Jul 2014 10:55:45 +
From: ABEL Stephane 175950 stephane.a...@cea.fr
To: gromacs.org_gmx-users@maillist.sys.kth.se
gromacs.org_gmx-users@maillist.sys.kth.se
Hi,
I want do an analysis of my simulation with the tool g_chi.
The problem is, that the optional output options don't work.
I use the following command:
g_chi -s config.gro -f traj.xtc -oh -all
and all I get are the standard output files chi.log and order.xvg.
I am not sure if it has
On 7/2/14, 9:22 AM, Dawid das wrote:
2014-07-02 13:50 GMT+02:00 Justin Lemkul jalem...@vt.edu:
The problems almost certainly stem from the manipulations you've made to
the angles and dihedrals. I don't understand why you've commented some of
them out. For instance, the first angle that
Beside that, why do you say that 978-992 are bonded? According to visual
inspection of mCherry7-solv-ion.gro there is no connection between them (as
it should be) and also in mCherry7.top there is no bonding parameter for
them.
2014-07-02 15:22 GMT+02:00 Dawid das add...@googlemail.com:
Excuse me but I don't think we understand each other. If there are three
atoms for instance and two of them are bonded and the third is not then how
can I obtain or derive parameters for them? That is what I do not
understand.
2014-07-02 15:29 GMT+02:00 Dawid das add...@googlemail.com:
Beside
On 7/2/14, 9:29 AM, Dawid das wrote:
Beside that, why do you say that 978-992 are bonded? According to visual
inspection of mCherry7-solv-ion.gro there is no connection between them (as
it should be) and also in mCherry7.top there is no bonding parameter for
them.
Inspection of a coordinate
Justin Lemkul jalemkul@... writes:
On 7/2/14, 3:31 AM, Emma Ahlstrand wrote:
Hi,
I have a problem with that the order of atoms in my topology does not
match the order of atoms in the gro-file.
I use amber99sb and I have built itp-files on my own for the molecules
that are not present
On 7/2/14, 9:48 AM, Emma A wrote:
Justin Lemkul jalemkul@... writes:
On 7/2/14, 3:31 AM, Emma Ahlstrand wrote:
Hi,
I have a problem with that the order of atoms in my topology does not
match the order of atoms in the gro-file.
I use amber99sb and I have built itp-files on my own for
Dear all,
I want to simulate graphite in water, for which i am trying to create a
topology file for graphite. As its .rtp file cannot be written correctly, i
tried to use g_x2top command following the steps given in following tutorial.
http://chembytes.wikidot.com/grocnt
But I think this
Dear Justin,
Thank you very much for your reply. I have tried the converter but I think
I don't have enough experience to get the CHARMM files working properly
with the converter. If I sent you the files, would it be possible to do it
for me or guide me through it?
Thanks again,
Nicholas
On
Without seeing the full contents of all the files, none of this really makes
sense. If you can provide a link to download the full (1) topology and all
related .itp files, (2) coordinates, and (3) .mdp files, I will take a look.
-Justin
Hi again,
thanks a lot for taking your time.
Here
On 7/2/14, 11:17 AM, Emma A wrote:
Without seeing the full contents of all the files, none of this really makes
sense. If you can provide a link to download the full (1) topology and all
related .itp files, (2) coordinates, and (3) .mdp files, I will take a look.
-Justin
Hi again,
thanks a
On 7/2/14, 9:56 AM, #SUKRITI GUPTA# wrote:
Dear all,
I want to simulate graphite in water, for which i am trying to create a
topology file for graphite. As its .rtp file cannot be written correctly, i
tried to use g_x2top command following the steps given in following tutorial.
On 7/2/14, 10:55 AM, Nikolaos Michelarakis wrote:
Dear Justin,
Thank you very much for your reply. I have tried the converter but I think
I don't have enough experience to get the CHARMM files working properly
with the converter. If I sent you the files, would it be possible to do it
for me
Hi all,
I have just ran a CG MD with the Martini force field, and I was wondering if
it’s possible to transform this CG trajectory back to a FG trajectory? If it’s
possible, are there any available tutorials I can follow? If not, please guide
me on the commands and modules required to execute
On 7/2/14, 11:48 AM, Yip Yew Mun wrote:
Hi all,
I have just ran a CG MD with the Martini force field, and I was wondering if
it’s possible to transform this CG trajectory back to a FG trajectory? If it’s
possible, are there any available tutorials I can follow? If not, please guide
me on
Hey Mark,
This might be a a dumb question, but over the official release download
links on the gromacs website, it still says: Please note that these are
not yet regarded as production quality, pending further testing, but the
code is now feature-stable.
Is this a typo because I thought the
On Jul 2, 2014 6:44 PM, Ali Khan ak...@virginia.edu wrote:
Hey Mark,
This might be a a dumb question, but over the official release download
links on the gromacs website, it still says: Please note that these are
not yet regarded as production quality, pending further testing, but the
code
Hi,
The warnings are not a problem - gmx view does not get as much love as the
rest of the project!
Mark
On Jul 2, 2014 11:23 AM, Luís Pereira luisp2...@gmail.com wrote:
Hi,
Thank you for this new version!
When compiling we've got these warnings:
attribute warn_unused_result
Thank you Sir. Sorry for the late reply. So, the changes like dihedral
angle for C8-C9=C10-C11 should be 180 instead of 0 in trans state. Are
there any other adjustments I should make to build the trans lipid isomer
topology from cis? Thank you for your valuable time and concern.
On Mon, Jun 16,
I know this is a silly question but in the downloads section when I click
to download it the new window opens and 0bit tar file is downloaded.I
switched to windows but even then the new tab doesn't show anything.I don't
understand why is this happening.
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The link is correct, something must be broken on your side. Try using e.g. wget:
$ wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz ls -l gromacs*.gz
--2014-07-02 22:34:44-- ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz
= `gromacs-5.0.tar.gz'
Resolving
Maybe something on your end is blocking ftp connections. You can download
from a mirror such as:
http://fossies.org/linux/privat/gromacs-5.0.tar.gz
If you download from a mirror make sure to check the md5sum.
On Wed, Jul 2, 2014 at 4:36 PM, Szilárd Páll pall.szil...@gmail.com wrote:
The link
Yeah apparently the ftp connection is blocked.I actually forgot that.Thanks
for the help.
On Thu, Jul 3, 2014 at 2:16 AM, Roland Schulz rol...@utk.edu wrote:
Maybe something on your end is blocking ftp connections. You can download
from a mirror such as:
Dear gmx users,
The g_polystat tool arranges the Rg eigen vectors in the descending order.
We cannot see how a particular eigen vector (one along the X-axis) varies
with time. We can obviously comment the section of the g_polystat code to
avoid the sorting. Is there a reason, why do we sort the
On 7/2/14, 4:36 PM, Szilárd Páll wrote:
The link is correct, something must be broken on your side. Try using e.g. wget:
$ wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz ls -l gromacs*.gz
--2014-07-02 22:34:44-- ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz
=
On Wed, Jul 2, 2014 at 11:08 PM, Justin Lemkul jalem...@vt.edu wrote:
On 7/2/14, 4:36 PM, Szilárd Páll wrote:
The link is correct, something must be broken on your side. Try using e.g.
wget:
$ wget ftp://ftp.gromacs.org/pub/gromacs/gromacs-5.0.tar.gz ls -l
gromacs*.gz
--2014-07-02
Thanks a lot, Justin. It's much clearer, but one last question: If the
coordinates in sample.gro extracted from xtc trajectory using trjconv (
without any application of pbc) are unwrapped, why almost all of them
happen to lie in the box, as can be seen in the following snapshot? I would
expect
On 7/2/14, 6:45 PM, Chetan Mahajan wrote:
Thanks a lot, Justin. It's much clearer, but one last question: If the
coordinates in sample.gro extracted from xtc trajectory using trjconv (
without any application of pbc) are unwrapped, why almost all of them
happen to lie in the box, as can be
I ran the md5sum but it does not match with any of the hashes.What should I
do now?
On Wed, Jul 2, 2014 at 5:55 PM, Szilárd Páll pall.szil...@gmail.com wrote:
On Wed, Jul 2, 2014 at 11:08 PM, Justin Lemkul jalem...@vt.edu wrote:
On 7/2/14, 4:36 PM, Szilárd Páll wrote:
The link is
Dear gromacs users,
I’m following this tutorial -
http://md.chem.rug.nl/cgmartini/index.php/proteins
in order to performed a CG simulation of an specific protein in a water box.
My problem is that when i’m trying to solvate my protein with genbox, by using
the next command:
genbox -cp
On Wed, Jul 2, 2014 at 6:55 PM, Harshkumar Singh harshsingh2...@gmail.com
wrote:
I ran the md5sum but it does not match with any of the hashes.What should I
do now?
Which file from which server (/which URL) did you download? What md5 did
you get?
Roland
On Wed, Jul 2, 2014 at 5:55 PM,
Never mind.
I used editconf before the energy-minimisation on vacuum (specifying the
size-box) and now, when i used genbox on the ’new’ structured it worked :D
--
Carlos Navarro Retamal
Bioinformatic engineer
Ph.D(c) in Applied Science, Universidad de Talca, Chile
Center of Bioinformatics
*Fatal error:*
25 particles communicated to PME node 2 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in dimension x.
This usually means that your system is not well equilibrated.
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Dear Justin,
Thanks for the reply but I am writing the .n2t file still getting the error
that Could not find force field 'graphite_oplsaa' in current directory,
install tree or GMXDATA path. What should I do? Moreover i don't think that
n2t file tells program to use graphite_oplsaa force
hello gromacs users
i am working on protein ligand compex with popc membrane for ligand
prepration from where i can get conf.gro file
because i am using conf.gro file from gromacs folder (tutor folder -water )
gromacs 4.5.7.
kindly help
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