Check this page for clarification
http://www.gromacs.org/Documentation/Errors#X_particles_communicated_to_PME_node_Y_are_more_than_a_cell_length_out_of_the_domain_decomposition_cell_of_their_charge_group
I guess this issue was also addressed before :
On 6/15/12 4:08 AM, Seera Suryanarayana wrote:
Dear all gromacs users,
While i am running the commond trjconv -f
1AKI_full.trr -s 1AKI_b4full.tpr -o final.pdb -dump 500 i am getting the
following warning.
WARNING no output, last frame read at t=10
Kindly tell
Have you incorrectly changed the numbers in the topology, the difference in the
number is 8, so it appears your coordinate file contains 8 more atoms than the
topology. You will have to work out how that is.
Catch ya,
Dr. Dallas Warren
Drug Discovery Biology
Monash Institute of Pharmaceutical
There is no GROMACS tool that repairs incomplete structures, but you can
find other programs that can do it. Some of them have been previously
posted in this list (try a search on it). Personally I've used Swiss PDB
viewer, which is useful to add missing atoms.
Javier
El 06/06/12 07:42,
I use MacroMolecular Builder for all sorts of things, including filling in
missing atoms.
Erik
6 jun 2012 kl. 08.59 skrev Javier Cerezo:
There is no GROMACS tool that repairs incomplete structures, but you can find
other programs that can do it. Some of them have been previously posted in
It seems that redefinition comes from including tow different ions.itp
files, here:
; Include topology for ions
#include gromos43a1.ff/ions.itp
#include ions.itp
Javier
El 06/06/12 10:51, Seera Suryanarayana escribió:
Dear all gromacs users,
After added
The error itself is self explanatory, there are no 22 atoms in your protein
structure, that suppose to be there. If you want to ignore those atoms when you
build your topology you can use the -missing option when you run pdb2gmx. But
if you need all the atoms you better construct a complete
On 4/06/2012 5:05 PM, Seera Suryanarayana wrote:
Dear all gromacs users,
While i am running pdb2gmx commond i
am getting following error.
Fatal error:
There were 22 missing atoms in molecule Protein_chain_A, if you want
to use
this incomplete topology.
I
I guess you have duplicate the moleculetype entries for CU1 in your topology
file. Check your topology file again. You can not have more than one
moleculetype definition per molecule type.
Cheers,
Emmanuel
=
Emmanuel Birru
PhD
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Seera Suryanarayana [paluso...@gmail.com]
Sent: Friday, May 25, 2012 6:23 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] Regarding error
Dear all gromacs users,
On 5/25/12 1:23 AM, Seera Suryanarayana wrote:
Dear all gromacs users,
While i am using the commond pdb2gmx -f
4E82.pdb -o 4E82.gro -p 4E82.top.I am getting the following warnings and
errors.
Warning: Residue EME21 in chain has different type (Other)
On Thu, May 24, 2012 at 10:20 AM, Seera Suryanarayana
paluso...@gmail.comwrote:
Dear all gromacs users,
while running the command grompp -c
1UZ9_em.gro -p 1UZ9.top -o 1UZ9_b4pr.tpr -f pr.mdp i am getting the
following error.
On 5/22/12 2:00 PM, Seera Suryanarayana wrote:
Dear all gromas users,
While i am running the grompp -c 1UZ9_em.gro -p 1UZ9.top -o 1UZ9_b4pr.tpr -f
pr.mdp after first mdrun command i got the following error.
File input/output error:
pr.mdp
Is there any explanation why is this happening?
Hi Seera
As the error message is telling you, the molecule type CU1 is defined
more than once along your topology. Check it, locate the [ moleculetype
] sections and verify that CU1 is defined only once. If that does not
solve the problem, you can post you topology here so that we can try to
Hi Suryanarayana,
http://www.gromacs.org/Documentation/Errors is where i'd start. But to help
you along this error suggests that you have a different number of atoms in
your coordinate file(.gro) than your topology(.top) suggests. Often this can
be caused by adding or removing ions or solvent
On Fri, May 18, 2012 at 12:20 PM, Seera Suryanarayana
paluso...@gmail.comwrote:
Dear all,
While i am running gromacs software i am getting following
error.Let me know that error how to over come.
Fatal error:
Residue 'CSD' not found in residue topology database
First read:
On 18/05/2012 4:50 PM, Seera Suryanarayana wrote:
Dear all,
While i am running gromacs software i am getting following
error.Let me know that error how to over come.
Fatal error:
Residue 'CSD' not found in residue topology database
Please search for your own answers before
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
On 5/11/2011 1:05 AM, kirubakaran palani wrote:
Dear All
Could any one help me to solve this error in gromacs 4.5.5 version. I
am running dynamics on apo protein and the protein shows negative
charge of -6 (after choosing OPLS-AA force filed) and when i was
neutralizing the -6 with +6 and
Meenakshi wrote:
Hi,
I am doing MD simulation of protein-ligand system using G53a6 as
forcefield. I got the ligand.itp file for ffG53a6 from the ATB
(Automated Topology Builder) server. I included the ligand.itp in the
.top file, generated an octahedron solvation box, solvated it and did
Anamika Awasthi wrote:
Dear friends
when I am trying command editconf, it is showing error
File input/output error
I have protein of 700 amino acids and its of inverted T shape and we
are giving boxtype dodecahedron.
input command is:
editconf_d -bt dodecahedron -f input.gro -o
On 13/04/2010 1:49 PM, Jignesh Patel wrote:
Hello,
while I am running grompp command, I am getting following error.
Opening library file /usr/local/gromacs/share/gromacs/top/ff_dum.itp
Generated 837 of the 2346 non-bonded parameter combinations
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