Hello,
I am running a equilibration simulation for ionic liquids at 400 K.
I am getting following note.
The sum of the two largest charge group radii (0.213127) is larger than
rlist (1.00) - rvdw (0.90)
Could you tell what is the problem? I am using Gromacs VERSION 4.5.5 .
I
On 10/31/13 10:30 AM, Nilesh Dhumal wrote:
Hello,
I am running a equilibration simulation for ionic liquids at 400 K.
I am getting following note.
The sum of the two largest charge group radii (0.213127) is larger than
rlist (1.00) - rvdw (0.90)
Could you tell what is the
Could you tell how can I get rid of following warning?
WARNING 1 [file test.top, line 263]:
The bond in molecule-type BMI between atoms 10 C10 and 23 H23 has an
estimated oscillational period of 1.2e-03 ps, which is less than 5 times
the time step of 1.0e-03 ps.
Maybe you forgot to
On 10/31/13 11:40 AM, Nilesh Dhumal wrote:
Could you tell how can I get rid of following warning?
WARNING 1 [file test.top, line 263]:
The bond in molecule-type BMI between atoms 10 C10 and 23 H23 has an
estimated oscillational period of 1.2e-03 ps, which is less than 5 times
the
Hello,
I am doing energy minimization for my system. I am getting following
warnings
Warning: atom name 20 in p2.top and p2.pdb does not match (C - S20)
Warning: atom name 21 in p2.top and p2.pdb does not match (C2 - O21)
Warning: atom name 22 in p2.top and p2.pdb does not match (N3 - O22)
On 9/22/13 7:13 PM, Nilesh Dhumal wrote:
Hello,
I am doing energy minimization for my system. I am getting following
warnings
Warning: atom name 20 in p2.top and p2.pdb does not match (C - S20)
Warning: atom name 21 in p2.top and p2.pdb does not match (C2 - O21)
Warning: atom name 22 in
On 9/22/13 8:54 PM, Nilesh Dhumal wrote:
Sorry to send email directly to your email address. Because of attachments
it not going through gmx_users.
The proper protocol is to post the files via publicly accessible URL so that
anyone interested in helping may assist.
attached the topology
Sorry to paste big files here. (.pdb file and processed.top )
pdb file.
TITLE Protein
REMARKTHIS IS A SIMULATION BOX
CRYST1 34.775 34.775 34.775 90.00 90.00 90.00 P 1 1
MODEL1
ATOM 1 C EMI 1 4.659 30.489 15.747 1.00 0.00
ATOM 2 C2
On 9/22/13 9:18 PM, Nilesh Dhumal wrote:
Sorry to paste big files here. (.pdb file and processed.top )
pdb file.
TITLE Protein
REMARKTHIS IS A SIMULATION BOX
CRYST1 34.775 34.775 34.775 90.00 90.00 90.00 P 1 1
MODEL1
ATOM 1 C EMI 1 4.659
Thanks.
I have total 128 EMI and 128 ETS. To find the solution I test for 2 EMI
and 2 ETS.
How can I define for 128 EMI and 128 ETS ?
Nilesh
On 9/22/13 9:18 PM, Nilesh Dhumal wrote:
Sorry to paste big files here. (.pdb file and processed.top )
pdb file.
TITLE Protein
REMARKTHIS
On 9/22/13 9:32 PM, Nilesh Dhumal wrote:
Thanks.
I have total 128 EMI and 128 ETS. To find the solution I test for 2 EMI
and 2 ETS.
How can I define for 128 EMI and 128 ETS ?
List 128 EMI consecutively, followed by 128 ETS consecutively, and make a
[molecules] directive analogously.
Dear Justin
I did minimization with the newest version of gromacs (4.6.3).
But, unfortunately, problem was not solved.
Best wishes for you.
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
* Please search the archive at
Dear Justin
Very thanks for your reply.
You said I suspect your Gromacs version is somewhat outdated, as recent
versions account for periodicity when
making this check. I used 4.5.5 version of gromacs. What version of
gromacs is more appropriate for my case.
Based on your suggestion, I used
Dear Justin
About following warning in grompp using
WARNING 1 [file em.mdp]:
The sum of the two largest charge group radii (6.940482) is larger than
rlist (1.20)
You said You probably have molecules split across PBC in the input
coordinate file. here's nothing wrong in that case
I mention
On 9/16/13 7:37 AM, shahab shariati wrote:
Dear Justin
About following warning in grompp using
WARNING 1 [file em.mdp]:
The sum of the two largest charge group radii (6.940482) is larger than
rlist (1.20)
You said You probably have molecules split across PBC in the input
coordinate
On 9/16/13 3:06 AM, shahab shariati wrote:
Dear Justin
Very thanks for your reply.
You said I suspect your Gromacs version is somewhat outdated, as recent
versions account for periodicity when
making this check. I used 4.5.5 version of gromacs. What version of
gromacs is more appropriate for
Dear gromacs users
My system contains 3 components: DOPC cholesterol lipids + drug + water
molecules.
In minimization step, when I use
grompp -f em.mdp -c system.gro -p topol.top -o em.tpr,
I encountered with following note and warning:
WARNING 1 [file em.mdp]:
The sum of the two largest
Dear gromacs users
Nember of groups in each of charge groups is less than or equal 3.
charge groups in my itp files are as follows:
DOPC.itp:
[ atoms ]
; nr type resnr residue atom cgnr
Dear gromacs users
I used -maxwarn option, but after using this command:
mdrun -s em.tpr -o em.trr -c em.gro -e em.edr -g em.log
I encountered with:
Fatal error:
There is no domain decomposition for 4 nodes that is compatible with the
given box and a minimum cell size of 6.61528 nm
Change the
On 9/15/13 3:44 AM, shahab shariati wrote:
Dear gromacs users
My system contains 3 components: DOPC cholesterol lipids + drug + water
molecules.
In minimization step, when I use
grompp -f em.mdp -c system.gro -p topol.top -o em.tpr,
I encountered with following note and warning:
WARNING 1
On 9/15/13 8:17 AM, shahab shariati wrote:
Dear gromacs users
I used -maxwarn option, but after using this command:
mdrun -s em.tpr -o em.trr -c em.gro -e em.edr -g em.log
I encountered with:
Fatal error:
There is no domain decomposition for 4 nodes that is compatible with the
given box
Thanks
On Tue, Jun 18, 2013 at 10:44 PM, massimo sandal deviceran...@gmail.comwrote:
2013/6/18 Hasni Arsad hasni.ar...@gmail.com
What should i do with this error massage:
Google it.
Program grompp, VERSION 4.6.2
Source code file:
:
-- Forwarded message --
From: Hasni Arsad hasni.ar...@gmail.com
Date: Tue, Jun 18, 2013 at 4:55 PM
Subject: Re: [gmx-users] grompp error
To: Discussion list for GROMACS users gmx-users@gromacs.org
What should i do with this error massage:
Program grompp, VERSION 4.6.2
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 hasni.ar...@gmail.com wrote:
Hi,
I got this error massage when execute this command- grompp -f em.mdp -c
solvated.pdb -p topol.top
Program grompp,
to suit your needs.
Mark
On Tue, Jun 18, 2013 at 10:57 AM, Hasni Arsad hasni.ar...@gmail.com wrote:
-- Forwarded message --
From: Hasni Arsad hasni.ar...@gmail.com
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 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
2013/6/18 Hasni Arsad hasni.ar...@gmail.com
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,
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,
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
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
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
On 9/29/12 12:55 PM, Ali Alizadeh wrote:
Dear All users
I have a system with 3 layers,
when i run grompp program, encounter with this error.
First and 3th layer is the same, and middle layer is water. what's
this error about?
grompp is looking for some group called 1 (the number one) but it
On 9/22/12 10:04 PM, Leandro Bortot wrote:
Dear all,
I am trying to do a glycoprotein simulation with GROMACS using the
AMBER99SB-ILDN forcefield together with GLYCAM06.
After constructing my glycoprotein grompp gives the following warning
for most of the atomtypes defined in the
Hi,
I am doing the simulation of KALP15 in DPPC following the Justin's tutorial.
For the step of solvation I ran this command:
# genbox -cp system.gro -cs spc216.gro -o system_solv.gro -p topol.top
The output of this step is as here:
Reading solute configuration
frame t= 1.000
Containing 17503
On 8/25/12 12:26 PM, Shima Arasteh wrote:
Hi,
I am doing the simulation of KALP15 in DPPC following the Justin's tutorial.
For the step of solvation I ran this command:
# genbox -cp system.gro -cs spc216.gro -o system_solv.gro -p topol.top
The output of this step is as here:
Reading solute
?
Sincerely,
Shima
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Shima Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS
users gmx-users@gromacs.org
Cc:
Sent: Saturday, August 25, 2012 8:59 PM
Subject: Re: [gmx-users] grompp in KALP15-DPPC
On 8/25/12
Arasteh shima_arasteh2...@yahoo.com; Discussion list for GROMACS users
gmx-users@gromacs.org Cc: Sent: Saturday, August 25, 2012 8:59 PM Subject:
Re: [gmx-users] grompp in KALP15-DPPC
On 8/25/12 12:26 PM, Shima Arasteh wrote:
Hi, I am doing the simulation of KALP15 in DPPC following the Justin's
Thanks for your reply.
Sincerely,
Shima
- Original Message -
From: Justin Lemkul jalem...@vt.edu
To: Discussion list for GROMACS users gmx-users@gromacs.org
Cc:
Sent: Saturday, August 25, 2012 9:16 PM
Subject: Re: [gmx-users] grompp in KALP15-DPPC
On 8/25/12 12:41 PM, Shima
Hello,
I have been running a simple simulation where I replace 150
water molecules in a waterbox with a lipid called DPC to create
micelles. This simulation is working fine and I'm getting decent
micelles fairly quickly. I am now trying to do the same, but with a
small peptide in the
On 7/23/12 9:54 AM, Christian Blouin wrote:
Hello,
I have been running a simple simulation where I replace 150
water molecules in a waterbox with a lipid called DPC to create
micelles. This simulation is working fine and I'm getting decent
micelles fairly quickly. I am now trying to
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
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
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
Hi
After:
pdb2gmx -f mymol.pdb -water tip3p
editconf -f conf.gro -bt dodecahedron -d 1.3 -o box.gro
genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro
I typed:
grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
where em.mdp is my energy minimization file and I got:
On 5/16/12 3:56 AM, Lara Bunte wrote:
Hi
After:
pdb2gmx -f mymol.pdb -water tip3p
editconf -f conf.gro -bt dodecahedron -d 1.3 -o box.gro
genbox -cp box.gro -cs spc216.gro -p topol.top -o solvated.gro
I typed:
grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
where em.mdp is my
...@vt.edu
An: Lara Bunte lara.bu...@yahoo.de; Discussion list for GROMACS users
gmx-users@gromacs.org
CC:
Gesendet: 13:22 Mittwoch, 16.Mai 2012
Betreff: Re: [gmx-users] grompp Unkown bond_atomtype C2
On 5/16/12 3:56 AM, Lara Bunte wrote:
Hi
After:
pdb2gmx -f mymol.pdb -water tip3p
On 5/16/12 8:05 AM, Lara Bunte wrote:
Hi
in my .rtp file I wrote in the [ atoms ] block
C2 CN1A0.7481 1
but in the atomtypes.atp file I wrote
CN1A12.01100
So I declared it. So what do you mean with such an atom type doesn't exist?
Neither of those actions constitutes
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
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
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
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
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
*De:* Justin A. Lemkul jalem...@vt.edu
*Para:* Eduardo Oliveira eduardo...@yahoo.com.br; Discussion list for
GROMACS users gmx-users@gromacs.org
*Enviadas:* Terça-feira, 3 de Abril de 2012 15:54
*Assunto:* Re: [gmx-users
Ok, thanks for the advice and sorry for sending the attached file.
De: Justin A. Lemkul jalem...@vt.edu
Para: Discussion list for GROMACS users gmx-users@gromacs.org
Enviadas: Terça-feira, 3 de Abril de 2012 16:51
Assunto: Re: [gmx-users] grompp error
*De:* Justin A. Lemkul jalem...@vt.edu
*Para:* Discussion list for GROMACS users gmx-users@gromacs.org
*Enviadas:* Terça-feira, 3 de Abril de 2012 16:51
*Assunto:* Re: [gmx-users] grompp error
Eduardo Oliveira wrote:
Thanks!
Please keep the discussion
Ok, thanks again. That actually worked.
De: Justin A. Lemkul jalem...@vt.edu
Para: Discussion list for GROMACS users gmx-users@gromacs.org
Enviadas: Terça-feira, 3 de Abril de 2012 18:30
Assunto: Re: [gmx-users] grompp error
Eduardo Oliveira wrote:
Ok
On 26/03/2012 4:13 PM, Jackson Chief wrote:
The missing residues correspond to a loop that connects two alpha
helices. The C-terminal end of one helix, and N-terminal end of the
other helix contain a random coil. After energy minimization, the
coils are extended in space and not connected.
I made a model of a receptor protein, bilayer, and solvent. My protein
contains a 20 residue gap. This gap corresponds to a region of the protein
that had been digested by trypsin before crystallization. The trypsin
digestion has no affect on receptor activity experimentally. I performed
energy
On 26/03/2012 12:20 PM, Jackson Chief wrote:
I made a model of a receptor protein, bilayer, and solvent. My
protein contains a 20 residue gap. This gap corresponds to a region
of the protein that had been digested by trypsin before
crystallization. The trypsin digestion has no affect on
The missing residues correspond to a loop that connects two alpha helices.
The C-terminal end of one helix, and N-terminal end of the other helix
contain a random coil. After energy minimization, the coils are extended
in space and not connected. I visualized this by looking at the .gro file
in
Hey,
The problem is likely that pdb2gmx created the bond. It will have given a
long bond warning. You can add a ter statement in the pdb file at the break.
Cheers,
Tsjerk
On Mar 26, 2012 5:49 AM, Mark Abraham mark.abra...@anu.edu.au wrote:
On 26/03/2012 12:20 PM, Jackson Chief wrote: I made
- Ursprüngliche Message -
Von: Mark Abraham mark.abra...@anu.edu.au
An: Discussion list for GROMACS users gmx-users@gromacs.org
CC:
Gesendet: 21:41 Mittwoch, 7.März 2012
Betreff: Re: [gmx-users] grompp - Group protein not found
On 8/03/2012 4:31 AM, Peter C. Lai wrote:
Check the molecules section
Greetings
Lara
- Ursprüngliche Message -
Von: Mark Abraham mark.abra...@anu.edu.au
An: Discussion list for GROMACS users gmx-users@gromacs.org
CC:
Gesendet: 21:41 Mittwoch, 7.März 2012
Betreff: Re: [gmx-users] grompp - Group protein not found
On 8/03/2012 4:31 AM, Peter C. Lai wrote
I trying to do an NVT simulation of a peptide in water with the following mdp
parameters:
title = GROMOS53A6 NVT equilibration
define = -DPOSRES ; position restrain the protein
; Run parameters
integrator = md; leap-frog integrator
nsteps = 5
Hi D_Roy,
The warning message is quite self-explanatory. Do read beyond the word
WARNING. As for the other question, the constraint algorithm stands apart
from the forcefield, unlike many other options. You can safely use Lincs
with G536.
Cheers,
Tsjerk
On Mar 17, 2012 10:31 AM, D_Roy
-users] grompp - Group protein not found
On 8/03/2012 4:31 AM, Peter C. Lai wrote:
Check the molecules section at the bottom of your top file. Each molecule
entry there should match the corresponding name given to it in the molecule's
own topology (the name under [moleculetype]).
Those names
Greetings
Lara
- Ursprüngliche Message -
Von: Mark Abrahammark.abra...@anu.edu.au
An: Discussion list for GROMACS usersgmx-users@gromacs.org
CC:
Gesendet: 21:41 Mittwoch, 7.März 2012
Betreff: Re: [gmx-users] grompp - Group protein not found
On 8/03/2012 4:31 AM, Peter C. Lai wrote
Hi
I create a file pr.mdp for equilibrating the water around my molecule and used
after that the command
grompp -f pr.mdp -p topol.top -c em.gro -o pr.tpr
And I got tthe error:
Fatal error:
Group protein not found in index file.
Group names must match either [moleculetype] names
or custom
Check the molecules section at the bottom of your top file. Each molecule
entry there should match the corresponding name given to it in the molecule's
own topology (the name under [moleculetype]).
On 2012-03-07 05:13:11PM +, Lara Bunte wrote:
Hi
I create a file pr.mdp for
On 8/03/2012 4:31 AM, Peter C. Lai wrote:
Check the molecules section at the bottom of your top file. Each molecule
entry there should match the corresponding name given to it in the molecule's
own topology (the name under [moleculetype]).
Those names can match and this error arise because
Ahh, case sensitivity?
Protein vs. protein?
On 2012-03-08 07:41:15AM +1100, Mark Abraham wrote:
On 8/03/2012 4:31 AM, Peter C. Lai wrote:
Check the molecules section at the bottom of your top file. Each molecule
entry there should match the corresponding name given to it in the
molecule's
On 8/03/2012 7:59 AM, Peter C. Lai wrote:
Ahh, case sensitivity?
Protein vs. protein?
No.
Mark
On 2012-03-08 07:41:15AM +1100, Mark Abraham wrote:
On 8/03/2012 4:31 AM, Peter C. Lai wrote:
Check the molecules section at the bottom of your top file. Each molecule
entry there should match
Hi
I used the command
grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
and got the error
Source code file: /home/adrian/src/gromacs-4.5.5/src/gmxlib/statutil.c, line:
819
Invalid command line argument:
em.tpr
What is the problem here?
Greetings
Lara
--
gmx-users mailing list
Lara Bunte wrote:
Hi
I used the command
grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
and got the error
Source code file: /home/adrian/src/gromacs-4.5.5/src/gmxlib/statutil.c, line:
819
Invalid command line argument:
em.tpr
What is the problem here?
The command posted
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
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
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
Justin A. Lemkul jalem...@vt.edu 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
Dear all,
I launch those commands for few models :
pdb2gmx -f 2it7-10_bestene1mc-SC.pdb -o 2it7-10_bestene1mc-SC.gro -p
2it7-10_bestene1mc-SC.top -ignh -missing
editconf -f 2it7-10_bestene1mc-SC.gro -o 2it7-10_bestene1mc-SC-box.gro -d 2.0
-c -bt cubic
grompp -c
pitheve...@free.fr wrote:
Dear all,
I launch those commands for few models :
pdb2gmx -f 2it7-10_bestene1mc-SC.pdb -o 2it7-10_bestene1mc-SC.gro -p
2it7-10_bestene1mc-SC.top -ignh -missing
editconf -f 2it7-10_bestene1mc-SC.gro -o 2it7-10_bestene1mc-SC-box.gro -d 2.0
-c -bt cubic
grompp
: Mardi 17 Janvier 2012 15:12:58
Objet: Re: [gmx-users] grompp g96angle types error
pitheve...@free.fr wrote:
Dear all,
I launch those commands for few models :
pdb2gmx -f 2it7-10_bestene1mc-SC.pdb -o 2it7-10_bestene1mc-SC.gro -p
2it7-10_bestene1mc-SC.top -ignh -missing
editconf -f 2it7
Envoyé: Mardi 17 Janvier 2012 15:30:08
Objet: Re: [gmx-users] grompp g96angle types error
pitheve...@free.fr wrote:
The problem seems to be between 3 S of CYS residues. I only use the 20 usual
residues and with no modifications.
An angle involving three S atoms? That should never occur
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 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
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
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
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
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
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
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--- 11年11月25日，周五, Gianluca Santoni gianluca.sant...@ibs.fr 写道：
发件人: Gianluca Santoni gianluca.sant...@ibs.fr
主题: Re: [gmx-users] grompp error
收件人: Discussion list for GROMACS users gmx-users
11月25日，周五, Gianluca Santoni gianluca.sant...@ibs.fr 写道：
发件人: Gianluca Santoni gianluca.sant...@ibs.fr
主题: Re: [gmx-users] grompp error
收件人: Discussion list for GROMACS users gmx-users@gromacs.org
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
Here is the detailed info about my setup:
System:64-bit Linux
GMX version:4.5.4
I know that windows and linux have different line end format and I didn't edit
my text files using editor on windows,but all on linux.
My goal is to simulate membrane protein embeded in lipid bilayer,I don't have
Here is the detailed info about my setup:
System:64-bit Linux
GMX version:4.5.4
I know that windows and linux have different line end format and I
didn't edit my text files using editor on windows,but all on linux.
Which editor? Problems in principle could arise from your encodings
setup,
I was trying to setup a simulation for membrane in DPPC lipid bilayer following
this tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
I successfully generated the .gro file for the system.But when I tried grompp
to generate the .tpr
On 24/11/2011 3:45 PM, 杨伟 wrote:
I was trying to setup a simulation for membrane in DPPC lipid bilayer
following this tutorial:
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/membrane_protein/index.html
I successfully generated the .gro file for the system.But when I
Hi [insert name here],
Try putting an empty gurgle.dat in your working directory to see if that is
the problem. If it's not, can you provide additional information regarding
your system and gromacs installation?
Cheers,
Tsjerk
On Nov 24, 2011 5:50 AM, 杨伟 20104227...@suda.edu.cn wrote:
I was
Hi Justin and Mark,
Thank you so much for your replies. Mark, would you mind clarifying what
you mean? What exactly should I be looking for in the ffbonded.itp file?
I'm not sure why those bonded parameters in particular were overridden... I
didn't intend to modify anything!
Perhaps it would
Olivia Waring wrote:
Hi Justin and Mark,
Thank you so much for your replies. Mark, would you mind clarifying what
you mean? What exactly should I be looking for in the ffbonded.itp file?
I'm not sure why those bonded parameters in particular were
overridden... I didn't intend to modify
Olivia Waring wrote:
Yes, it's the same error.
About the bond types: should they be defined as opls_* in ffbonded.itp,
aminoacids.rtp, both, or somewhere else entirely?
The bonds are named in the aminoacids.rtp file, they are defined in
ffbonded.itp. Use names in the .rtp, types in
Dear Gromacs users,
First of all, many thanks to Justin for his assistance with my previous
question.
I have defined a new residue type in the oplsaa force field, changing the
aminoacids.rtp file accordingly. pdb2gmx worked just fine; but when I try
to preprocess, I get the following output:
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