-users/2011-February/058868.html
Cheers,
EB
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Seera Suryanarayana
Sent: Tuesday, 19 June 2012 4:50 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] Regarding error.
Dear all gromacs users
Dear all gromacs users,
While i am running the commond "mdrun
-deffnm nvt" i am getting the following error.
Fatal error:
1 particles communicated to PME node 1 are more than 2/3 times the cut-off
out of the domain decomposition cell of their charge group in
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 tel
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 me how to overcome this error.
Suryanarayana Seer
On 6/11/12 4:37 AM, Seera Suryanarayana wrote:
Dear Justin sir,
I am simulating a protein 1AKI.pdb which is example of
your tutorial.I am doing simulations as your tutorial.I didnt get any errors
upto the commond "grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o
e
Dear Justin sir,
I am simulating a protein 1AKI.pdb which is example of
your tutorial.I am doing simulations as your tutorial.I didnt get any
errors upto the commond "grompp -f minim.mdp -c 1AKI_solv_ions.gro -p
topol.top -o em.tpr".After this as your tutorial i used the common
Behalf Of Seera Suryanarayana
Sent: Friday, 8 June 2012 3:32 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] Regarding error
Dear all gromacs users,
While running the grompp commond after
addition of counter ions i am getting the following error
Dear all gromacs users,
While running the grompp commond after
addition of counter ions i am getting the following error.
Fatal error:
number of coordinates
in coordinate fil
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
Dear all gromacs users,
After added the counter ions to the top
file and further i used 'grompp' commond,i got the following error.
Fatal error:
moleculetype CU1 is
redefin
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
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, Seera
Dear all gromacs users,
I have 1VZV.pdb file, in that file HIS231
has incomplete ring as N atom is missing.Can i add N atom to the .pdb file
if possible how can i add that atom to .pdb file.
Suryanarayana Seera,
PhD student,
India.
--
gmx-users mailing listg
Dear all gromacs users,
While i am running pdb2gmx commond i am
getting following error.
Fatal error:
incomplete ring in HIS231
Kindly tell me how to overcome this error and how to
Dear Mark,
What type of file i have to check for missing of atoms.
Thanks and regards.
--
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Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before p
Dear all gromacs users,
I tried the grompp and i got the following error.
Fatal error:
moleculetype CU1 is redefined.
Is there any explanation why is thid happening?
I've checked [moleculetypes] in topology files and there are not duplicated.
I would appreciate any help. Iam new in using
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 w
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 wont ignore the 22 missing atoms by using -missing commo
t: Monday, 4 June 2012 3:52 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] Regarding error
Dear all gromacs users,
While i am running gromacs software i am getting following error.Let me
know that error how to over come.
Fatal error:
There were 22 missing atoms in molecule Protein_chain
Dear all gromacs users,
While i am running gromacs software i am getting following error.Let me
know that error how to over come.
Fatal error:
There were 22 missing atoms in molecule Protein_chain_A, if you want to use
this incomplete topology.
Suryanarayana Seera,
PhD student,
Hyderabad,
I
w.pharm.monash.edu.au<http://www.pharm.monash.edu.au/>
From: gmx-users-boun...@gromacs.org [mailto:gmx-users-boun...@gromacs.org] On
Behalf Of Seera Suryanarayana
Sent: Tuesday, 29 May 2012 5:02 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] Regarding error
Dear all gromacs users,
I tr
Dear all gromacs users,
I tried the "grompp -c 3I40_ion.gro -p 3I40.top -o
3I40_b4em.tpr -f em.mdp" and i got the following error.
Option Filename Type Description
-f em.mdp Input
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) fr
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
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) from starting
residue ALA1 (Protein).
Warning: Residue
On Thu, May 24, 2012 at 10:20 AM, Seera Suryanarayana
wrote:
> 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.
>
> File
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.
File input/output error:
pr.mdp
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?
I
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?
I would appreciate any help.I am new in using MD and
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
Dear all gromacs users,
I tried the grompp and i got the following
error.
Fatal error:
number of coordinates in coordinate file (1UZ9_ion.gro, 41103)
does not match topology (1UZ9.top, 41100)
Is there any explanation why is thid happening?
I would
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
Dear all gromacs users,
I tried the grompp and i got the
following error.
Fatal error:
moleculetype CU1 is redefined.
Is there any explanation why is thid happening?
I would appreciate any help. Iam new in using MD and gromac in particular.
Suryanarayana Se
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 posti
On Fri, May 18, 2012 at 12:20 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
First read:
http://www.grom
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
Suryanarayana Seera,
PhD student,
Hyderabad,
India.
--
gmx-users mailing listgmx-users@gromacs.
On Mon, Apr 30, 2012 at 11:50 AM, seera suryanarayana
wrote:
> 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
>
>
http://www.gromac
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.
--
gmx-users mailing listgmx-users@gromacs.org
http://l
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 gen
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 generating the genion.tpr file there it shows "No such
m
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 generating the genion.tpr file there it shows "No such
m
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
th
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
the grompp step before
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 box
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 box.gro -c -d 10.0
with regard
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
--
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
---
Program grompp, VERSION 4.0.5
Source cod
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