Respected Sir,
While i am running the gromacs software to simulate
the protein i am getting the following error.
Fatal error:
Residue 'GNP' not found in residue topology database
Suryanarayna Seera,
PhD student.
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On Mon, Apr 30, 2012 at 11:50 AM, seera suryanarayana
paluso...@gmail.comwrote:
Respected Sir,
While i am running the gromacs software to simulate
the protein i am getting the following error.
Fatal error:
Residue 'GNP' not found in residue topology database
Please anybody help me
I'm trying to simulate a protein-ligand complex system using GROMACS 4.5.3
and Amber03 forcefield.
In this system, a carbocationic intermediate was used as ligand
C - C+ - C - C - O-PP (Carbocationic intermediate)
│
C
I tried to obtain
On Fri, Apr 27, 2012 at 5:13 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 4/27/12 12:09 PM, Steven Neumann wrote:
On Fri, Apr 27, 2012 at 4:38 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
On 4/27/12 11:34 AM, Steven Neumann wrote:
On Fri, Apr 27,
On 30/04/2012 6:34 PM, Steven Neumann wrote:
On Fri, Apr 27, 2012 at 5:13 PM, Justin A. Lemkul jalem...@vt.edu
mailto:jalem...@vt.edu wrote:
On 4/27/12 12:09 PM, Steven Neumann wrote:
On Fri, Apr 27, 2012 at 4:38 PM, Justin A. Lemkul
jalem...@vt.edu
On Mon, Apr 30, 2012 at 9:39 AM, Mark Abraham mark.abra...@anu.edu.auwrote:
On 30/04/2012 6:34 PM, Steven Neumann wrote:
On Fri, Apr 27, 2012 at 5:13 PM, Justin A. Lemkul jalem...@vt.edu wrote:
On 4/27/12 12:09 PM, Steven Neumann wrote:
On Fri, Apr 27, 2012 at 4:38 PM, Justin A.
Follow this link
http://www.gromacs.org/Documentation/Errors#Number_of_coordinates_in_coordinate_file_does_not_match_topology.
On Mon, Apr 30, 2012 at 3:19 PM, seera suryanarayana paluso...@gmail.comwrote:
Dear all gromacs users,
I tried the grompp and i got the following error.number
Hi,
we had similar trouble some time ago, and we could solve it by using a
good PBC atom. Make sure that your pbc_atom is in the very center of
your membrane.
Btw, using distance to compare with cylinder is a bad test, since it
does something very different (the distance is the same at
On 30/04/2012 7:49 PM, seera suryanarayana wrote:
Dear all gromacs users,
I tried the grompp and i got the following error.number of
coordinates in coordinate file (4INS_b4ion.gro, 90396)
does not match topology (4INS.top,
90393).
Dear GROMACS users,
I have a nanoparticle (perfect sphere) and want to enclose it into a
rhombic dodecahedron. For this purpose I use the following command lines
editconf_d4.5.5 -f nano.gro -bt dodecahedron -d 1 -c -o nano_box.gro
grompp_d4.5.5 -f em.mdp -c nano_box.gro -p nano.top -o
Hi
I have the command
trjconv -n index.ndx -f molecule.pdb -o output.pdb
that don't work because of the missing topol.tpr file. You wrote:
Supply your .pdb file to the -s flag
Where exactly do I have to write -s in my command?
Thanks for help
Greetings
Lara
- Ursprüngliche
Hi
Just out of curiosity: When will be the next release for a new version of
Gromacs with extended manual?
Greetings
Lara
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Please search the archive at
On 4/30/12 11:41 AM, Lara Bunte wrote:
Hi
I have the command
trjconv -n index.ndx -f molecule.pdb -o output.pdb
that don't work because of the missing topol.tpr file. You wrote:
Supply your .pdb file to the -s flag
Where exactly do I have to write -s in my command?
Anywhere.
you will have to find the parameters for a carbocation in this configuration
from someone who has derived them before, if acpype doesn't know about the
species in this configuration, or derive them yourself using ab
initio/semiempiracle methods (i.e. gaussian). Also remember you'll need angle
Hi!
Sorry for bugging you all once more, but the data from this survey is
critically important for all our future development and acceleration efforts
(not only GPUs), and that means it's important to _you_ :-)
So, if you haven't done so yet, please help make your needs heard by taking
just a
Dear Gromacs users,
I want to set up an umbrella sampling simulation of an Hypericin dimer.
I have created position restraint files for hypericin with genrestr and then
use it with the topology file, so I want to know if it is just restraining one
of the Hypericin Molecules or both of them?
Hi Justin
I got the error
Can not open file:
topol.tpr
if I type trjconv -n index.ndx -f molecule.pdb -o output.pdb -s
and I got the error
Can not open file:
traj.xtc
if I type trjconv -n index.ndx -f -s molecule.pdb -o output.pdb
What is the problem?
Greetings and thank you for
On 4/30/12 12:29 PM, Lara Bunte wrote:
Hi Justin
I got the error
Can not open file:
topol.tpr
if I type trjconv -n index.ndx -f molecule.pdb -o output.pdb -s
and I got the error
Can not open file:
traj.xtc
if I type trjconv -n index.ndx -f -s molecule.pdb -o output.pdb
What is the
On 4/30/12 12:26 PM, Hovakim Grabski wrote:
Dear Gromacs users,
I want to set up an umbrella sampling simulation of an Hypericin dimer.
I have created position restraint filesfor hypericin with genrestr and then
use it with the topology file, so I want to know if it is just restraining one
of
On 4/30/12 11:51 AM, Lara Bunte wrote:
Hi
Just out of curiosity: When will be the next release for a new version of
Gromacs with extended manual?
Sometime soon. What exactly are you expecting to be new in the manual? There
will be some new features, but from the development history
* How to use
gromacs using openmpi*
Hello all, i am an undergraduate student here at VIT University
Vellore,INDIA, I m trying to run mdrun on a cluster using openmpi, so for
that i have used Ubuntu 11.04 server edition , and made a cluster
Hi all,
Thank you for your time! It seems that the code was not compiled with the
--enable-mpi option. We have recompiled, and everything works now.
Andrew
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Please search the archive at
Hi
I trying to install the OpenMM to so run gromacs using GPU, but when I set
the locals variables and type: sudo ./install.sh
It's says:
SUDO_USER=laboratorio24
PWD=/home/laboratorio24/OpenMM4.0-Linux64/python
File setup.py, line 165
print %s % outputString
^
SyntaxError:
Hi,
Is it possible to compute the ion conductivity using any of the existing
Gromacs tools? Ion conductivity is proportional to the current-current
(auto)correlation function.
For example, the current J_z(t) along z can be written as the sum of the
products of charge and z-component of the
Hi Justin
First:
It works, thank you :-)
Second:
You wrote:
Again, as has been stated several times, giving any Gromacs program a
command line option (like -s or -f) in the absence of an explicit file
name, will cause the program to look for a default file name (which are
listed in the
On Mon, 2012-04-30 at 13:49 -0400, Andrew DeYoung wrote:
Hi,
Is it possible to compute the ion conductivity using any of the existing
Gromacs tools? Ion conductivity is proportional to the current-current
(auto)correlation function.
For example, the current J_z(t) along z can be
Hello GMX users,
does anyone that dealt with Charmm before knows how to translate the NBFIX
section into a Gromacs ff format? After convertion from KCal to KJ, does it go
into [pairtypes]?
I see that it concerns to corrections in LJ interactions, however the charmm
documentation seems a bit
NBFIXes haven't been used in charmm for a long time (1998), although
current versions still read topologies containing those records. Perhaps you
should reparameterize your molecule with a more current version? (Or start with
the coordinate file and use pdb2gmx with the converted ff). The only
Dear Gromacs Users,
I used the command genbox -cs spc216.gro -o box1.g96 -p topol.top -box 3 3
10 to create box of 3010 water molecules. However, now I need to create a
same size box with only 846 water molecules. Please help me to do this.
Thanks,
Cuong
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gmx-users mailing list
On 4/30/12 10:02 PM, cuong nguyen wrote:
Dear Gromacs Users,
I used the command genbox -cs spc216.gro -o box1.g96 -p topol.top -box 3 3 10
to create box of 3010 water molecules. However, now I need to create a same size
box with only 846 water molecules. Please help me to do this.
Use the
On 1/05/2012 12:02 PM, cuong nguyen wrote:
Dear Gromacs Users,
I used the command genbox -cs spc216.gro -o box1.g96 -p topol.top
-box 3 3 10 to create box of 3010 water molecules. However, now I
need to create a same size box with only 846 water molecules. Please
help me to do this.
Use a
Thanks,
I tried to add -maxsol 846 to the command and got the box with 846 water
molecules. However, when I use VMD to visualize the box, these molecules
concentrate on 1/3 the box space. I do need the molecules to spread out
whole box.
Cheers,
Cuong
2012/5/1 Justin A. Lemkul jalem...@vt.edu
On 1/05/2012 12:20 PM, cuong nguyen wrote:
Thanks,
I tried to add -maxsol 846 to the command and got the box with 846
water molecules. However, when I use VMD to visualize the box, these
molecules concentrate on 1/3 the box space. I do need the molecules to
spread out whole box.
So next
Easiest solution can think of, make box that is of sufficient size the when
filled contains 846 waters, fill with waters, use editconf to scale the box
size to that which you require, run EM to get the waters back to the dimensions
they should be.
Catch ya,
Dr. Dallas Warren
Medicinal
Please keep discussions on the emailing list so others at a later point can use
the material if needed. Unless of course you are paying me for my comments ;-)
What you really should do is go back to the start, fresh directory with nothing
in it and start from the start. Follow the steps
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