gt; >
> >
> > -- Forwarded message --
> > From: Hasni Arsad
> > Date: Tue, Jun 18, 2013 at 4:55 PM
> > Subject: Re: [gmx-users] grompp error
> > To: Discussion list for GROMACS users
> >
> >
> > What should i do with this error
Thanks
On Tue, Jun 18, 2013 at 10:44 PM, massimo sandal wrote:
> 2013/6/18 Hasni Arsad
>
> > What should i do with this error massage:
> >
>
> Google it.
>
>
> > Program grompp, VERSION 4.6.2
> > Source code file:
> > /home/hasni/Bioinformatics/gromacs-4.6.2/src/kernel/grompp.c, line: 563
> >
>
2013/6/18 Hasni Arsad
> What should i do with this error massage:
>
Google it.
> Program grompp, VERSION 4.6.2
> Source code file:
> /home/hasni/Bioinformatics/gromacs-4.6.2/src/kernel/grompp.c, line: 563
>
> Fatal error:
> number of coordinates in coordinate file (solv.gro, 50853)
>
What should i do with this error massage:
Program grompp, VERSION 4.6.2
Source code file:
/home/hasni/Bioinformatics/gromacs-4.6.2/src/kernel/grompp.c, line: 563
Fatal error:
number of coordinates in coordinate file (solv.gro, 50853)
does not match topology (topol.top, 50816)
For more
suit your needs.
Mark
On Tue, Jun 18, 2013 at 10:57 AM, Hasni Arsad wrote:
>
>
> -- Forwarded message --
> From: Hasni Arsad
> Date: Tue, Jun 18, 2013 at 4:55 PM
> Subject: Re: [gmx-users] grompp error
> To: Discussion list for GROMACS users
>
>
&
GROMACS is not yet magic. You used an atom type not found in your force
field. Over to you. :-)
Mark
On Jun 18, 2013 5:23 AM, "Hasni Arsad" wrote:
> Hi,
>
> I got this error massage when execute this command- grompp -f em.mdp -c
> solvated.pdb -p topol.top
>
>
>
> Program grompp, VERSION 4.6.2
>
On 1/2/13 10:01 AM, Mijiddorj wrote:
Hello all, I am new user of gromacs. I am doing Tutorial 1. When I run
grompp, following problem occurred:Program grompp, VERSION 4.5.3Source code
file: toppush.c, line: 1987Fatal error:No such moleculetype CL-For more
information and tips for troubleshootin
On 10/22/12 8:46 PM, Nur Syafiqah Abdul Ghani wrote:
Dear All,
Right now i want to do another simulation which is water and co-solvent,HFIP.
I get the small compound file from
http://compbio.biosci.uq.edu.au/atb/download.py?molid=6187#files
I need to used the all atom one and the force field t
On 17/05/2012 11:47 PM, Lara Bunte wrote:
Hello
After
grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
I got the error:
Incorrect number of parameters - found 2, expected 4 or 4 for U-B.
I thought that this could be an inconsistency be declaring the functions, but
in my topology
On 5/17/12 9:47 AM, Lara Bunte wrote:
Hello
After
grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
I got the error:
Incorrect number of parameters - found 2, expected 4 or 4 for U-B.
I thought that this could be an inconsistency be declaring the functions, but
in my topology I
On 4/22/12 11:49 PM, Nilesh Dhumal wrote:
Hello,
I am doing solvation dynamics for my system.
When I am running grompp command I get the error.
grompp -f md.mdp -c solvent-bmi-pf6-128.pdb -p
solvent-bmi-pf6-128.top -o md-rerun.tpr
Fatal error:
No such combination rule 0
I using
Ok, thanks again. That actually worked.
De: Justin A. Lemkul
Para: Discussion list for GROMACS users
Enviadas: Terça-feira, 3 de Abril de 2012 18:30
Assunto: Re: [gmx-users] grompp error
Eduardo Oliveira wrote:
> Ok, thanks for the advice and sorry
*De:* Justin A. Lemkul
*Para:* Discussion list for GROMACS users
*Enviadas:* Terça-feira, 3 de Abril de 2012 16:51
*Assunto:* Re: [gmx-users] grompp error
Eduardo Oliveira wrote:
> Thanks!
>
Please keep the discussion on the list. From your .mdp file:
t
Ok, thanks for the advice and sorry for sending the attached file.
De: Justin A. Lemkul
Para: Discussion list for GROMACS users
Enviadas: Terça-feira, 3 de Abril de 2012 16:51
Assunto: Re: [gmx-users] grompp error
Eduardo Oliveira wrote:
> Tha
tems.
-Justin
*De:* Justin A. Lemkul
*Para:* Eduardo Oliveira ; Discussion list for
GROMACS users
*Enviadas:* Terça-feira, 3 de Abril de 2012 15:54
*Assunto:* Re: [gmx-users] grompp error
Eduardo Oliveira w
Probably consult the tutorials to determine what T-coupling groups to use.
Generally, Water_and_ions with a separate Protein as 2 T-coupling groups when
dealing with a globular protein in water, but you will have to determine if
that is appropriate for your particular system (i.e. if there are lig
Eduardo Oliveira wrote:
Hi all,
After i ran grompp I've the following message:
Fatal error:
3 atoms are non part of any of the T-coupling groups
It is probably in refference to the 3 CL atoms i've introduced into the
system to neutralize my protein charge. Here are the command lines for
ge
Lara Bunte wrote:
Yes it was included in forcefield.itp
Only pdb2gmx uses .rtp files (see the manual).
Thanks for your help
Know I got the error
No default Fourier Dih. types
What should I do?
You need a corresponding [dihedraltypes] for all dihedrals in the system. The
error i
Lara Bunte wrote:
Hi
I used the command
grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
and get this errors:
ERROR 1 [file flavin.rtp, line 1]:
Invalid directive bondedtypes
ERROR 2 [file flavin.rtp, line 7]:
Not enough parameters
I know where this error occurs from but
niaz poorgholami wrote:
Dear all
I am using Gromacs 4.5.3 to simulate a system including:
CNT+water+surfactant and I want to
use opls force field for my whole system.
so far I have done following things:
1.I copied oplsaa.ff folder in my working directory.
2.I added following lines to atomnam
niaz poorgholami wrote:
Dear gmx users,
I am using gromacs 4.5.3 to simulate CNT in water. up to now I have done
these things:
1. I used packmol to create my PDB file and the used editconf to change
PDB to gro file.
2. I copied oplsaa.ff folder in my working directory
3. I added following l
g 100101,china
--- 11年11月25日，周五, Gianluca Santoni 写道：
发件人: Gianluca Santoni
主题: Re: [gmx-users] grompp error
收件人: "Discussion list for GROMACS users"
日期: 2011年11月25日,周五,下午4:21
The most reasonable thing is that there is a typo in your .mdp or in your .top
files.
Check where you've
biology & Immunology
INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES
NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china
--- 11年11月25日，周五, Gianluca Santoni 写道：
发件人: Gianluca Santoni
主题: Re: [gmx-users] grompp error
收件人: "Discussion list for GROMACS users"
日期: 2011年11月25
The most reasonable thing is that there is a typo in your .mdp or in
your .top files.
Check where you've written "Ptotein" instead of Protein
On 11/25/11 4:09 PM, yp sun wrote:
Dear Sir'
When I ran the grompp as following
grompp -v -f md.mdp -c pr.gro -p RI-10.top -o md.tpr
a error information
On 25/11/2011 7:09 PM, yp sun wrote:
Dear Sir'
When I ran the grompp as following
grompp -v -f md.mdp -c pr.gro -p RI-10.top -o md.tpr
a error information appeared:
Program grompp, VERSION 3.3.1
Source code file: readir.c, line: 789
Fatal error:
Group Ptotein not found in indexfile
Maybe you hav
Mark Abraham wrote:
; water topology
#include "tip3p.itp"
grompp is not detecting the change of [moleculetype], so you will have
to look at the contents of that tip3p.itp and see why. I think you will
need to #include some standard force field to get the water parameters.
Put the #include
On 8/10/2011 12:35 AM, Chunxia Gao wrote:
Dear all,
I generated the molecule topology from antechamber and then coverted to
gromcas topology.
When I tried to use grompp first it gave me this error : there is no such molecule type
SOL, so I checked the topology file and found out there was n
bob dole wrote:
Hello,
I have conducted several runs in which I pull one peptide away from
another; however, the peptide being pulled gets visually “stretched” out
when viewing the trajectory in VMD and DSSP confirms this. I came across
this recent post
(http://lists.gromacs.org/pipermail
eate an index group to
accommodate the system. In other cases, it means you're using a group that is
simply not applicable.
-Justin
--- On *Tue, 5/31/11, Justin A. Lemkul //* wrote:
From: Justin A. Lemkul
Subject: Re: [gmx-users] Grompp error on index file
To: "
e
to identify it as a carbohydrate. In fact, the index.file identified it as a
carbohydrate. I borrowed the nvt.mdp from the Lysozyme tutorial authored by
you. Thanks.
--- On Tue, 5/31/11, Justin A. Lemkul wrote:
From: Justin A. Lemkul
Subject: Re: [gmx-users] Grompp error on index file
To: "
Mr Bernard Ramos wrote:
Hi everyone!
I added a residue on the gromacs 4.5.3 I have. I followed the
instructions as indicated in the "Adding A Residue to a Force Field"
with this link
_http://www.gromacs.org/Documentation/How-tos/Adding_a_Residue_to_a_Force_Field?highlight=adding+residue_.
Nilesh Dhumal wrote:
Thanks Justin,
Here I pasted water.top
;
; File 'water.top' was generated
; By user: ndhumal (36026)
; On host: c63
; At date: Thu Apr 21 14:52:38 2011
;
; This is your topology file
; Protein
;
; Include forcefield parameters
#include
Thanks Justin,
Here I pasted water.top
;
; File 'water.top' was generated
; By user: ndhumal (36026)
; On host: c63
; At date: Thu Apr 21 14:52:38 2011
;
; This is your topology file
; Protein
;
; Include forcefield parameters
#include "ffoplsaa.itp"
; Include
Nilesh Dhumal wrote:
Hello,
I am trying to run a simulation for flexiable water. I use the parameters
from J. Chem. Phys. (2006),124,024503 paper and made a spc_fw.itp file.
; Derived from parsing of runfiles/alat.top.orig
[ defaults ]
; nbfunccomb-rule gen-pairs fudgeLJ
Hyunjin Kim wrote:
Dear,
When I generated bond parameters as following and ran "grompp", then I had
an error messages "No default Angle types"
[ angletypes ]
; i j k functh0 cth ub0 cub
OST CST OST 5 180.25104.0 0.0 0.0
CS
trevor brown wrote:
Dear users,
I have the following error with grompp before minimization.
I defined opls_996 for C atom by myself.
How did you define it? Whatever you did wasn't sufficient.
Any suggetions to solve it?
With respect to the rest, I already replied about those:
http://lis
On 16/01/2011 7:09 PM, bharat gupta wrote:
Hi
I am using gromacs 4.5.3 ... I am using OPLSS force field in
simulation and while issuing grompp command for energy minimzation I
am getting an error "No molecule type NA+ exists" ... I used NA+ while
issuing genion command ..., can anybody tell me
On 24/12/2010 7:01 AM, Sergio Manzetti wrote:
Dear users,
I made the a topology, but when I grompp for EM I get this weird message:
Fatal error:
Syntax error - File forcefield.itp, line 12
Last line read:
'Buckingham 1 no 1.0 1.0'
Found a second defaults
my command was:
/share/apps/gromacs-4.5.2/bin/grompp_mpi -f md.mdp -c
../../membed_17_npt.gro.884814.gro -t ../../membed_17_npt.trr.884814.trr -e
../../membed_17_npt.edr.884814.edr -p topol_protein_dppc_sol3_22.top -n
index.ndx -o md_0_1_22.tpr
the name of the edr file (and other NPT outputs) is
On 22/11/2010 11:03 PM, Adva Suez wrote:
Hello,
I'm using your KALP in DPPC tutorial to figure out how to simulate a
molecule in a membrane in GROMACS. I'm using version 4.5.2 and from
some reason I got an error in grompp whe trying generate md_0_1.tpr.
the error is:
Program grompp_mpi, VERS
Roland Schulz wrote:
Please make sure that the error exists in the latest version. Either
4.5.1 or if you know how please check the latest GIT version
from release-4-5-patches. If you still get the error with the latest
version, please file a bugzilla report and attach all required files.
Please make sure that the error exists in the latest version. Either 4.5.1
or if you know how please check the latest GIT version
from release-4-5-patches. If you still get the error with the latest
version, please file a bugzilla report and attach all required files.
On Tue, Sep 28, 2010 at 9:01
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Hello,
I am really curious that amber has support for Room Temperature Ionic
liquids ? Can you please provide me a reference how this force field
works for this kind of liquids.
/Flo
On 09/28/2010 03:01 PM, Alep Latep wrote:
> Dear Gromacs Users
Moeed wrote:
Dear gmx users,
I am trying to compress a single polymer chain. grompp is giving the
error below:
Program mdrun, VERSION 4.0.7
Source code file: ns.c, line: 2299
Fatal error:
One of the box vectors has become shorter than twice the cut-off length
or box_yy-|box_zy| or box_zz
shahid nayeem wrote:
HI
I am using Cytochrome-C pdb 1hrc.pdb. In pdb2gmx it does not gives
any eror using ffG43a1. .top file produced shows all bonds (Fe & SD of
MET 80 and Fe & NE2 of HIS 18) using spec.dat file but all the error
lines does not have bond/angle nomenclature such as
809 810
HI
I am using Cytochrome-C pdb 1hrc.pdb. In pdb2gmx it does not gives
any eror using ffG43a1. .top file produced shows all bonds (Fe & SD of
MET 80 and Fe & NE2 of HIS 18) using spec.dat file but all the error
lines does not have bond/angle nomenclature such as
809 810 2gb_30
810 8
shahid nayeem wrote:
Hi Justin
These errors are from bond between MET/HIS residue and Heme group of
my protein. I checked for all these nine errors of bond and angle in
th file ffG43a1bon.itp and I couldnt find these defined in this file.
Using other options of force field also gives error at
Hi Justin
These errors are from bond between MET/HIS residue and Heme group of
my protein. I checked for all these nine errors of bond and angle in
th file ffG43a1bon.itp and I couldnt find these defined in this file.
Using other options of force field also gives error at some point.
waiting for
shahid nayeem wrote:
Dear All
I used the following command sequentially to prepare file for energy
minimization and subsequent MD run.
1. pdb2gmx -f *.pdb -o seq.gro -p seq.top
2. editconf -f seq.gro -o seq_box.gro -d 1.0 -bt cubic
3. genbox -cp seq_box.gro -cs spc216.gro -o seq_b4ion.gro -p
Arik Cohen wrote:
In continuation with my previous e-mail, I'm sorry to continue bothering
you with this but after reevaluating, it seems that problem might just
be with the amber forcefield after all as I manged to run grompp just
fine and to start the minimization by applying the OPLS forc
In continuation with my previous e-mail, I'm sorry to continue bothering
you with this but after reevaluating, it seems that problem might just
be with the amber forcefield after all as I manged to run grompp just
fine and to start the minimization by applying the OPLS forcefield(with
another
Thanks again for the ultrafast response.
1. The extra '.' is a typo. (I apologize for that). In the command the
file name appears as 1bgq_Complex_b4ion.tpr
in addition, Both the single precision and double
precision(grompp_d) gives this error.
The compilation was done with gcc-4.4.3 wit
On 25/04/2010 6:28 AM, Arik Cohen wrote:
Thank a lot for your very fast response !. Here are the requested details:
1. Version 4.07 is being used.
2. Upgrading from version 4.04 to 4.07 doesn't help.
3. The grompp command given is:
grompp -f MDP/em.mdp -c 1bgq_Complex_b4ion.pdb -p 1bgq_Comple
I suppose the next set of questions to ask would be:
1. How was Gromacs compiled? What options were specified?
2. Does every instance of grompp fail? Do other inputs work? What does "grompp
-h" do?
3. Does grompp seg fault with totally different systems (different force
fields)?
-Justin
Thank a lot for your very fast response !. Here are the requested details:
1. Version 4.07 is being used.
2. Upgrading from version 4.04 to 4.07 doesn't help.
3. The grompp command given is:
grompp -f MDP/em.mdp -c 1bgq_Complex_b4ion.pdb -p 1bgq_Complex.top
-o 1bgq_Complex_b4ion..tpr
4.
On 24/04/2010 7:28 AM, Arik Cohen wrote:
I'll be most thankful if any one would be able to help me with the
following problem.
Giving more complete information will give you a much better chance.
It's not our job to be the family doctor and ask questions :-)
What GROMACS version is it? Does
2009/11/18 qing yang
> Dear gmx-users,
>
> I am try to simulate the protein-drug, and have used drg.itp from prodrg
> server2,5(beta). I have also got pro.top from pdb2gmx programs. But when I
> issue a grompp command for minimization,grompp gives a fatal error.
>
> The error is:
>
> Error 0 [f
You include unk.itp but show us drg.itp. Perhaps you're looking at or
using the wrong file.
/Erik
qing yang skrev:
Dear gmx-users,
I am try to simulate the protein-drug, and have used drg.itp from
prodrg server2,5(beta). I have also got pro.top from pdb2gmx programs.
But when I issue a gro
qing yang wrote:
Dear gmx-users,
I am try to simulate the protein-drug, and have used drg.itp from prodrg
server2,5(beta). I have also got pro.top from pdb2gmx programs. But when
PRODRG topologies are often unsatisfactory with respect to charges and charge
groups assigned. Looking at the
afsaneh maleki wrote:
Hi,
I am working on memberane peptide simulation under lipid DOPC,i have
downloaded the lipid and dopc.itp from the same site,when i run grommp:
]grompp -f em.mdp -c complex.gro -o em.tpr -p complex.top
it gives me:
>Fetal error :
Atomtype LC3 not found! (this is
Cíntia C. Vequi-Suplicy wrote:
Hello,
I am trying to simulate a lipid membrane with Gromacs. I am trying to
generate the *.tpr file o run the simulation, but every time I use the
command grompp I got the following error:
checking input for internal consistency...
...ling /usr/bin/cpp
: No suc
nitu sharma wrote:
Dear MARK
Now the problem of matching of topology file and
coordinate file solved but the other two errors come during running
grompp in the second step of inflategro .
my command line is like this- grompp -f em.mdp -p topolinflate.top -c
inflated_syst
Both of those errors are telling you want you need to do. In your
topol_A.itp file, there are no parameters for a particular proper
dihedral. So, define one. Same with the next message. And it even
tells you which line the issue is on in the .itp file, so very easy to
track down which bonds are
nitu sharma wrote:
Dear all
I am doing simulation of membrane protein ,for this
first i did the concatanation of protein in lipid bilayer in proper
orientation after that I am using inflategro script of teleman sir
but after doing first step successfully I am getting probl
nitu sharma wrote:
Hello justin ,
thanks for ur previous suggestion . I am doing simulation of membrene
protein , as u suggest in previous mail to use gromos9653a6 forcefield
parameters in topology file of protein+lipid bilayer.
I have made topology accordingly like this-
; Include forc
nitu sharma wrote:
Dear all,
I am trying to do simulation of membrane protein with
lipid bilayer for this I have made topology file like this-
; topology for tap in 128 dmpc lipids plus water.
; rr1_A.itp and rr1_B.itp can be made in a straightforward manner with
pdb2gmx
Might I suggest that you refer to this webpage
http://wiki.gromacs.org/index.php/Errors
It would have answered both of your error questions you have posted.
Catch ya,
Dr. Dallas Warren
Department of Pharmaceutical Biology and Pharmacology
Pharmacy and Pharmaceutical Sciences, Monash University
Hello Madam,
Greetings from Pawan.
The solution for this is to edit the atom names as required such as replace
NTM with N4 in all the places wherever NTM occurs.
Similarly do this for all the atoms of the dppc lipid.
I think this is a probable solution.
I dont know how far I am right.
Regards,
P
Hi,
Greetings from Pawan.
Edit your lipid.itp file.
Comment or remove the lines :
[default]
1 1
Then grompp will work..
Regards,
Pawan
2009/3/30 nitu sharma
> Dear all ,
>
>
> I am trying to do simulation of DMPC lipid
> bilayer for this I
Dean Cuebas wrote:
Dear users,
I¹ve been trying to reproduce the GROMACS tutorial for Drug _ Enzyme Complex
I¹ve tried to get grompp to work, but I keep getting the following message:
___
creating statusfile for 1 node...
Back Off! I just ba
Protein_E 1
Protein_F 1
Protein_G 1
Protein_H 1
T80 92
QIU YI HUAN
A beginner of Gromacs user.
--- On Tue, 2/10/09, Justin A. Lemkul wrote:
From: Justin A. Lemkul
Subject: Re: [gmx-users] grompp error
To: scottieh...@yahoo.com, &
tein_G 1
Protein_H 1
T80 92
QIU YI HUAN
A beginner of Gromacs user.
--- On Tue, 2/10/09, Justin A. Lemkul wrote:
> From: Justin A. Lemkul
> Subject: Re: [gmx-users] grompp error
> To: scottieh...@yahoo.com, "Discussion list for GROMACS use
Q. Y. HUAN wrote:
Dear all.
I wanted to run grompp in order to perform Em, but it showed me this fatal
errer::
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
checking input for internal consistency...
calling /usr/bin/cpp...
processing topology...
Generated 332520 of the 332520 no
Sarah Witzke wrote:
Dear gromacs users,
I'm doing simulations of small molecules in lipid bilayers. Doing the
simulations with a DMPC bilayer works fine for all 4.x versions of gromacs. But
when I try to do an energy minimization of a POPC bilayer, grompp gives the
following error:
/people/d
In the manual, have a look at Table 5.4; you are missing lots of parameters
within the topology (masses, force constants for bonds and angles...)
-Justin
Oliver Masur wrote:
Hi,
i'm still trying to use the genbox command to put h2po4 (aka DHP) in the
box.
i've got a gro file for h2po4:*
*DH
hmm, okay, forget whatever you think I replied :)
On 11/5/08, Berk Hess <[EMAIL PROTECTED]> wrote:
>
> Hi,
>
> There is a bug in the 4.0 grompp which causes problems when you have two
> consecutive "blocks" with the same molecule type.
> You will have to merge them into one block.
>
> I have
Hi Supti,
> --
>
> Program grompp_d, VERSION 4.0
> Source code file: grompp.c, line: 352
>
> Fatal error:
> number of coordinates in coordinate file (file_b4em.gro, 46634)
> does not match topology (file.top, 9977)
> -
It's just wh
Hi,
There is a bug in the 4.0 grompp which causes problems when you have two
consecutive "blocks" with the same molecule type.
You will have to merge them into one block.
I have fixed this bug for the 4.0.1 release.
Berk
> Date: Wed, 5 Nov 2008 13:21:27 +0530
>
Your formatting is incorrect.
The .gro format is a very old GROMOS fixed format (not free format).
See the manual for the details:
http://www.gromacs.org/documentation/reference/online/gro.html
Thanks a lot. Now everything works perfectly!
/Andreas
_
Berk Hess wrote:
Hi,
Your formatting is incorrect.
The .gro format is a very old GROMOS fixed format (not free format).
See the manual for the details:
http://www.gromacs.org/documentation/reference/online/gro.html
Thanks for the link - I remember asking for it on this list years ago :-)
I've
Hi,
Your formatting is incorrect.
The .gro format is a very old GROMOS fixed format (not free format).
See the manual for the details:
http://www.gromacs.org/documentation/reference/online/gro.html
Berk.
> Date: Tue, 22 Apr 2008 12:12:17 +0200
> From: [EMAIL PROTECTED]
> To: gmx-users@gromacs.or
Justin A. Lemkul skrev:
Just thinking out loud, but maybe "Argon" is too long of a name for the
residues. The longest I think I've seen is 4 characters (something like LYSH
or ARGN, for example). Maybe the length of the name is throwing off the
formatting. Why don't you try again with a residu
Just thinking out loud, but maybe "Argon" is too long of a name for the
residues. The longest I think I've seen is 4 characters (something like LYSH
or ARGN, for example). Maybe the length of the name is throwing off the
formatting. Why don't you try again with a residue name of something like
I had similar memory related problems. Try compiling Gromacs with no
optimization and rerun the grompp.
On Feb 7, 2008 7:45 AM, David van der Spoel <[EMAIL PROTECTED]> wrote:
> Chris Neale wrote:
> > I have a large system of 0.7 million atoms. This system runs fine on
> > opterons with 4GB of ram
Chris Neale wrote:
I have a large system of 0.7 million atoms. This system runs fine on
opterons with 4GB of ram. However, grompp gives me an error that it has
run out of memory on a new IBM AIX system that we have with 46GB of ram.
Smaller systems work fine on both processors. In both cases I
Quoting Jens Pohl <[EMAIL PROTECTED]>:
> Hello!
>
> I've tried to prepare a file for the mdrun and when I use grompp I get the
> massage that there is a fatal error in grompp.c line or line 1109,
> respectively.
What command are you issuing? What's in the .mdp file? What is the *exact*
err
On 22 Jan 2008 11:10:47 -
"sarbani chattopadhyay" <[EMAIL PROTECTED]> wrote:
hi,
I am trying to run gromacs using charmm but I am facing the following
error while
running the "grompp" command
checking input for internal consistency...
calling /usr/local/bin/cpp...
topol.top:11:24: /
jahanshah ashkani wrote:
Please start a new email for a new topic, to help keep things organized.
> Dear users,
> I have got the following error when I run grompp:
> Fatal error:
> There were 2 errors in input file(s)
> I would be glad if you help me.
> Thank you very much.
This means there are
Dear users,
I have got the following error when I run grompp:
Fatal error:
There were 2 errors in input file(s)
I would be glad if you help me.
Thank you very much.
Jahanshah Ashkani,
PhD student of Biotechnology & Genetics,
University of the Western Cape,
Biotechnology Department,
Private Bag X
pragya chohan wrote:
hi ... when i run grompp i get an error " No such moleculetype Protein " ... i
included itp for ACE and AIB after generating them from PRODRG2 server... my top file is :
Check out
http://wiki.gromacs.org/index.php/Errors#Fatal_error:_No_such_moleculetype_XXX
Mark
__
ERROR: The cut-off length is longer than half the shortest box vector
or longer than the smallest box diagonal element. Increase the box
size or decrease rlist.
try to "Increase the box size or decrease rlist." <= as ERROR message suggests
On 10/9/07, pragya chohan <[EMAIL PROTECTED]> wrote:
Dhananjay wrote:
Hello all,
I am trying to minimise a structure having 3 chains and each of having
90 residues. While running grompp , I got following error.
Please tell me how to fix this error.
Thanking you in advance .
creating statusfile for 1 node...
checking input for internal con
Dhananjay wrote:
Hello all,
I am trying to minimise a structure having 3 chains and each of having
90 residues. While running grompp , I got following error.
Please tell me how to fix this error.
chapter 5.
wiki.gromacs.org
Thanking you in advance .
creating statusfile for 1 node...
: 305-904-2419 Office: 305-284-3938
From: [EMAIL PROTECTED] on behalf of Tsjerk Wassenaar
Sent: Tue 4/24/2007 12:34 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] grompp error
Hi Luciano,
Look in the topology file where your metal complex is
Hi Luciano,
Look in the topology file where your metal complex is defined (under
each [ ] section, but this seems to me to be a dihedral). You've not
given enough parameters for one of the bonded definitions.
Furthermore, it is likely that the error is in the .rtp entry,
assuming you generated on
type "which cpp" to know the location of cpp.
Another source of error could be your mdp file which is now in Windows'
format, using /r/n for a new line while Unix uses only /n.
Please use tools like dos2unix (a package shall be also available from
cygwin) to convert your mdp file.
Regards,
Ya
Thanks for the reply,
I have tried changing the mdp file so it looks for the cpp in /lib/cpp,
/lib/cpp.exe, /bin/cpp, and /bin/cpp.exe and all of these produce the same
message as below, that the cpp file does not exist. It had worked when I ran
a simulation before with the mdp file as /lib/c
toma0052 wrote:
Hello,
I just installed Gromacs on my windows machine under cygwin, and
everything seemed to go fine with the installation and whatnot. Initially,
when I tried to run a simulation, I obtained the error that Gromacs found the
number of coordinates in my .top file to be 0, bec
Am Donnerstag, 8. März 2007 schrieb best alep:
> I got this error everytime, after i change the value, there's still error
> message like this but with rcoulomb or rvdw values.
Which values did you change?
> "ERROR: The cut-off length is longer than half the shortest box vector or
> longer than
Hi Tsjerk:
thanks again for the full description of what i should to do.
I did it and grompp runs !
cheers
Maite
On 3/3/07, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote:
Hi Maite,
Indeed you shouldn't really run the lipids through pdb2gmx, but try to
obtain a .itp file for a lipid, match
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