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
>
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
Source code file: /gromacs-4.6.2/src/kernel/toppush.c, line: 1336
Fatal error:
Atomtype NPYL not found
For more information and tips for troubleshooting, plea
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
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 troubleshooting, please check the GROMACSwebsite at
htt
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
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 have function 4 (for improper dihedrals)
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
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 Gromacs VERSION 4.0.5.
What this error mean
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
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 genion and
grompp
genion_d -
"Justin A. Lemkul" wrote:
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
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
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 I don't know what is fa
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
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 atomname2type.n2t
Copls_9950
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
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 lines to atomname2type.n2t
C
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
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 have non-default goups in your
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
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 no
#include "tip3p.itp" . so I added this to
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
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/gmx-users/2011-Septembe
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_.
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.
I added the residue to residu
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
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 fudgeQQ
;1
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
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 SS FE 5
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
Dear users,
I have the following error with grompp before minimization.
I defined opls_996 for C atom by myself.
Any suggetions to solve it?
best
trevor
WARNING 1 [file ffbonded.itp, line 2703]:
Overriding Bond parameters.
old: 0.151 292880 0.151 292880
new: C C 1 0.14210478900
ERR
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
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 where am I going wrong??
--
Bharat
Ph.D. Can
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
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 directive.
I attached the topology here with t
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
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, VERSION 4.5.2
Source code file: enxio.c, line: 1097
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
Dear Gromacs Users and Developers,
I'm currently using Gromacs 4.5 on a Fedora 12 i686 to performed my ionic
liquid MD simulation using amber 99 force field. I got my topology from
topolbuild v 1.3. I successfully minimized both cation and anion separately
using cg and steep. Then I include the an
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
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 has become smaller t
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
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 seq.top
4. grompp -c s
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
I'll be most thankful if any one would be able to help me with the
following problem.
While running the grompp (in both single and double precision) command I
get a Segmentation fault (core dumped) error. The error persist even
after recompiling the GROMACS with gcc-4.4.3(previously I was runn
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
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 [file "unk.itp",line 4]
Not enough para
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
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 atomtype of the lipide)
This i
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
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 such file or directory
cpp exit code:
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
resemble
a nail.
From: gmx-users-boun...@gromacs.org
[mailto:gmx-users-boun...@gromacs.org] On Behalf Of nitu sharma
Sent: Friday, 24 April 2009 2:40 PM
To: gmx-users@gromacs.org
Subject: [gmx-users] grompp error
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_system.gro -o inflated-em.tp
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
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 problem in second step
i,e ene
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 problem in second step
i,e ene
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
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 forcefield parameters
#include
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
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, starting
; with a pdb fi
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 pawan ,
Thanks for your right suggestion bu t after editing lipid.itp the
another error comes like this-
processing topology...
Opening library file /usr/local/gromacs/share/gromacs/top/ffgmx.itp
Opening library file /usr/local/gromacs/share/gromacs/top/ffgmxnb.itp
Opening library fi
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