On 10/24/13 10:21 AM, felipe vasquez wrote:
Hi,
I chose group 0 (System), but I also tried others like 1 (Protein) or 2
(Protein+H) with the same result.
You don't want to embed ions into your protein or haphazardly into the system.
You'll start deleting random segments of molecules, or th
Hi,
I chose group 0 (System), but I also tried others like 1 (Protein) or 2
(Protein+H) with the same result.
Regards,
Andrés F.
*Andrés Felipe Vásquez J., MSc.*
Grupo de Fisiología Molecular
Subdirección de Investigación Científica y Tecnológica
Dirección de Investigación en Salud Pública
In
On 10/24/13 9:34 AM, felipe vasquez wrote:
Hi,
I have been trying to add ions to my system so as to make it neutral.
However, I always obtain the same result:
Solvent Group size (950) is not multiple of 9.
What group did you choose at the genion prompt?
The command I entered in this step
On 10/17/13 1:01 PM, sunyeping wrote:
Dear Gromacs users,
I am trying to add ions to my system using:genion -s ions.tpr -o solv_ions.gro
-p topol.top -pname NA -nname CL -np 8
but it returns a error message saying:
Fatal error:
No line with moleculetype 'SOL' found the [ molecules ] section
Hi Deepak,
You have to set the minimal distance between ions lower. Check the help of
genion.
Cheers,
Tsjerk
On Aug 28, 2013 8:04 AM, "Deepak Ojha" wrote:
Dear Gmxers,
I want to simulate 5M nabr aqueous solution.To add the ions I use genion
command and add 22 na and br ions
respectively to t
On 5/3/13 11:27 AM, Ewaru wrote:
Hi,
Just wondering. My system shows this: "System has non-zero total charge:
11.98"
and thus, I use the command as below to add 12 Cl to the protein:
"genion -s ions.tpr -o m4_solv_ions.gro -p topol.top -pname NA -nname CL -nn
12"
However, when I checked
On 4/27/13 12:28 PM, Justin Lemkul wrote:
On 4/27/13 11:21 AM, Nathan Bullock wrote:
I am running genion neutralize the charge of my protein.
I got an error that wasn't very descriptive
Fatal error:
Cannot read from input
The part of the script that called this program read as follows
/usr/l
On 4/27/13 11:21 AM, Nathan Bullock wrote:
I am running genion neutralize the charge of my protein.
I got an error that wasn't very descriptive
Fatal error:
Cannot read from input
The part of the script that called this program read as follows
/usr/local/gromacs-4.5.5/bin/grompp -f em.mdp -c fi
cience, into this forum.
With Regards
Abhishek Acharya
>
>
> From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on
> behalf of Abhishek Acharya [aacha...@iitk.ac.in]
> Sent: Friday, April 05, 2013 9:35 PM
> To: Discussion list for GROMACS use
ndian "science"
Best,
Felipe
From: gmx-users-boun...@gromacs.org [gmx-users-boun...@gromacs.org] on behalf
of Abhishek Acharya [aacha...@iitk.ac.in]
Sent: Friday, April 05, 2013 9:35 PM
To: Discussion list for GROMACS users
Subject: Re: [gm
> On 04/05/2013 09:09 PM, Warren Gallin wrote:
>> Don't you have to give tyne name of the positive and negative ions that
>> will be added by genion? Otherwise, how would it know?
>>
>> Warren Gallin
>
> No, it doesn't work either:
>
> genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutra
On Fri, Apr 5, 2013 at 3:09 PM, Warren Gallin wrote:
> Don't you have to give tyne name of the positive and negative ions that
> will be added by genion? Otherwise, how would it know?
>
>
Default names are used (see genion -h), and the default names are correct
for all force fields as of version
On 04/05/2013 09:09 PM, Warren Gallin wrote:
Don't you have to give tyne name of the positive and negative ions that will be
added by genion? Otherwise, how would it know?
Warren Gallin
No, it doesn't work either:
genion_mpi -s ions.tpr -o solv_ions.gro -p complex.top -neutral
-norandom -p
On Fri, Apr 5, 2013 at 3:05 PM, Albert wrote:
> Hello:
>
> I found that there would be some problem of genion in 4.6.1:
>
> grompp_mpi -f em.mdp -c solv.gro -p complex.top -o ions.tpr
>
> NOTE 1 [file complex.top, line 44008]:
> System has non-zero total charge: -11.00
> Total charge sho
On Fri, Apr 5, 2013 at 3:05 PM, Albert wrote:
> Hello:
>
> I found that there would be some problem of genion in 4.6.1:
>
> grompp_mpi -f em.mdp -c solv.gro -p complex.top -o ions.tpr
>
> NOTE 1 [file complex.top, line 44008]:
> System has non-zero total charge: -11.00
> Total charge sho
Don't you have to give tyne name of the positive and negative ions that will be
added by genion? Otherwise, how would it know?
Warren Gallin
On 2013-04-05, at 1:05 PM, Albert wrote:
> Hello:
>
> I found that there would be some problem of genion in 4.6.1:
>
> grompp_mpi -f em.mdp -c solv.gr
Hi there,
In addition to setting -pq to 2 as Justin said, you can set -conc to a
very low value such as 0.1 for neutralizing the system.
One more thing... genion apparently uses the box volume when
determining how many ions are necessary for getting a given ionic strength.
However,
On 9/9/12 7:53 AM, Matthias Ernst wrote:
Hi,
I just encountered (another) strange thing with genion.
I wanted to neutralized a system by adding Mg-Ions (charge in ions.itp: 2,
forcefield amber99sb), so I expected half of the system charge (-52) to be added
as ions. BUT it added the same amount
e Março de 2012 14:25
*Assunto:* Re: [gmx-users] genion
Eduardo Oliveira wrote:
> Hi all,
>
> I' ve stumbled upon a problem when i used genion to prepare my files.
Here's the comand line:
>
> genion_d -s sistema_stpr.tpr -o sistema_ions.gro -nname CL- -nn 3 -nq
Eduardo Oliveira wrote:
Hi all,
I' ve stumbled upon a problem when i used genion to prepare my files.
Here's the comand line:
genion_d -s sistema_stpr.tpr -o sistema_ions.gro -nname CL- -nn 3 -nq -1
-p sistema.toI
I've got this in return:
Fatal error:
Your solvent group size (73282) is
On 17/03/2012 4:57 PM, Wholly Peach wrote:
Will you please tell me where can I find the ions.itp file?
http://www.gromacs.org/Documentation/Terminology/Environment_Variables
Mark
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please sea
Will you please tell me where can I find the ions.itp file?
I am looking forward to getting your reply.
Wholly
From: Mark Abraham
To: Discussion list for GROMACS users
Sent: Saturday, 17 March 2012 3:55 PM
Subject: Re: [gmx-users] genion -pname no NA
On 17/03/2012 4:48 PM, Wholly Peach wrote:
Dear All,
I use the following to neutralize the charge
"genion -s ions.tpr -o 1AKI_solv_ions.gro -p topol.top -pname NA -nname CL -nn 8",
Then I do the following "grompp -f minim.mdp -c 1AKI_solv_ions.gro -p topol.top -o em.tpr"".
However the
Bharath.K. Chakravarthi wrote:
HI
I'm not sure about this kind of error but as per my knowledge the
problem might be with the parameter cpp in mdp file.
In my mdp file it is as follows
The problem is unrelated to cpp, since the error complained about the use of
"warnings" in the .mdp
manjula kasinathan wrote:
hi snip
Thank u. as per ur suggestion i added sodium ions to my protein.
then i carried out mdrun for energy minimization nsteps 3000 but i runs
only for 1108 steps. then i went to position restrain steps the command
i gave
grompp -f pr.mdp -c em
HI
I'm not sure about this kind of error but as per my knowledge the problem
might be with the parameter cpp in mdp file.
In my mdp file it is as follows
title = ecoli_nusG
cpp = /usr/bin/cpp
define = -DPOSRES
constraints = all-bonds
integrator = md
dt = 0.001 ; ps !
nsteps = 10 ; total 10
Justin A. Lemkul wrote:
Smiruthi Ramasubramanian wrote:
Justin,
I tried to use an index file with atom numbers of the water molecules
in the required volume.
But when I try to ionize the box, I get this error:
Fatal error:
The solvent group SOL is not continuous: index[717]=21689,
ind
Smiruthi Ramasubramanian wrote:
Justin,
I tried to use an index file with atom numbers of the water molecules in
the required volume.
But when I try to ionize the box, I get this error:
Fatal error:
The solvent group SOL is not continuous: index[717]=21689, index[718]=21696
This makes s
Justin,
I tried to use an index file with atom numbers of the water molecules in the
required volume.
But when I try to ionize the box, I get this error:
Fatal error:
The solvent group SOL is not continuous: index[717]=21689, index[718]=21696
This makes sense, but is there a way get around this
Smiruthi Ramasubramanian wrote:
I am simulating an ion channel and require help placing a concentration
of ions at one side of the box (below the membrane).
"Sidedness" is irrelevant in a periodic system; the water layers are continuous
with PBC.
SETUP: membrane + embedded protein in
leila karami wrote:
Hi
total charge of my system (pr-dna) is (-10). which is better in genion
command:
1) 10 Na or 2) 20 NA + 10 Cl
http://www.gromacs.org/Documentation/Gromacs_Utilities/genion
Additional ions model increased ionic strength. Whether or not that is "better"
is up to yo
leila karami wrote:
Hi
total charge of my system (pr-dna) is (-10). which is better in genion
command:
1) 10 Na or 2) 20 NA + 10 Cl
Only you can answer that, because only you know your objective.
Mark
--
gmx-users mailing listgmx-users@gromacs.org
http://lists.gromacs.org/mailman/list
Paymon Pirzadeh wrote:
Well, if I have understood your words properly,
apparently there is a problem in the first residue in amino terminal
which I treated the NH2 as a zwitterionic piece(+1), and gave the side
chain -1 charge. I thought it should add up to zero, but apparently it
does not:
Well, if I have understood your words properly,
apparently there is a problem in the first residue in amino terminal
which I treated the NH2 as a zwitterionic piece(+1), and gave the side
chain -1 charge. I thought it should add up to zero, but apparently it
does not:
1 opls_287 1ASP
Paymon Pirzadeh wrote:
Well, when I look into my .top file, almost no where I see closeness to
an integer (as close as you said 0.9998). It gets up to -1.05 or -0.91
sometimes. But I can not see a clear trend on where things go wrong. My
protein has only 37 amino acids with 451 atoms (including
Well, when I look into my .top file, almost no where I see closeness to
an integer (as close as you said 0.9998). It gets up to -1.05 or -0.91
sometimes. But I can not see a clear trend on where things go wrong. My
protein has only 37 amino acids with 451 atoms (including hydrogens).
I am not sure
Paymon Pirzadeh wrote:
Thanks for the tips!
But I still have problem with my added ion. Justin had told me that ion
names are force-field specific! Since I am using OPLSaa, I checked the
itp file for Na ion name, and it was Na+. I used this name with the
No, it's not. It's NA+. From ions.it
Thanks for the tips!
But I still have problem with my added ion. Justin had told me that ion
names are force-field specific! Since I am using OPLSaa, I checked the
itp file for Na ion name, and it was Na+. I used this name with the
-pname switch, but again during the grompp I ran into the following
Paymon Pirzadeh wrote:
Can I change the charge of Na ion added from +1 to +0.99 to cancel the
negative charge exactly? Does that hurt science or simulation?
It's probably irrelevant. The representation of "decimal" numbers on
computers can be inexact, such that things like 0.02 added to itself
Can I change the charge of Na ion added from +1 to +0.99 to cancel the
negative charge exactly? Does that hurt science or simulation?
Payman
On Tue, 2009-08-25 at 17:22 -0400, Justin A. Lemkul wrote:
>
> Paymon Pirzadeh wrote:
> > I realized sth about the previous error message I posted. In th
Hi,
To set things straight a bit.
>> "If you are using ion-related GROMACS tools, such as genion, you will need
>> to enter the AMBER ion definition to the ions.itp file in the "top"
>> directory of the GROMACS distribution."
>
> This isn't too tough, as all the parameters for the ions are includ
Andrew,
Just ran into this myself. If you read the notes on http://chemistry.csulb.edu/ffamber/#usage
closely, you'll find this little tid-bit:
"If you are using ion-related GROMACS tools, such as genion, you
will need to enter the AMBER ion definition to the ions.itp file in
the "top" di
drugdesign wrote:
Dear gromacs users,
I am using genion command to add ions to .tpr file which
was made for protein by use of amber03 force field.
In intial pdb file N-terminal amino acid is NHIE, but genion changes it to NHI, which isnot recognized by next pdb2gmx.
PDB format dictates 3 ch
Hi,
On Tuesday, 26. August 2008, Bhanu wrote:
> Hi,
> I'm using Gromacs 3.3.3, installed with double precision. When I run genion
> with this command:
>
> genion_d -s *.tpr -o *.gro -g genion.log -pot pot.pdb -p *.top -neutral
>
> the following error message was generated:
> --
Bhanu wrote:
Hi,
I'm using Gromacs 3.3.3, installed with double precision. When I run
genion with this command:
genion_d -s *.tpr -o *.gro -g genion.log -pot pot.pdb -p *.top -neutral
the following error message was generated:
--
Hi sh-karbalaee,
Well, running an MD simulation has nothing to do with genion per se.
But it's better not to have a net chare in your system. Therefore
you'd best add an ion (at the least) to your system with unit charge.
Whether you do that using genion or do it by hand, is entirely up to
you. Ch
Subhrangshu Supakar wrote:
Hi All !!
I have defined my own system which contains 200 water molecules, which I
can see in the .gro file. Then I created the .tpr file for 200 steps to
steep. In the confout file I can again see the 200 water molecules. But
When I am trying to replace the 200 wate
Narayanan Veeraraghavan wrote:
Hi,
I was wondering if there was a way to specify a minimum distance
between the counter-ion and solute, using Genion. There is a rmin
option, buts thats for the dist between the ions. But, I am interested
in the distance between ions and solute. Would appreciate an
Building
Tel:(+44) 151 795 5140
FAX:(+44) 151 794 5130
University of Liverpool
Crown St.,Liverpool L69 7ZB, U.K.
-Original Message-
From: [EMAIL PROTECTED] on behalf of Tsjerk Wassenaar
Sent: Thu 7/19/2007 7:53 AM
To: Discussion list for GROMACS users
Subject: Re: [gmx-users] genion - hangs
Hi Luciane,
David van der Spoel has replied saying:
there is a problem compiling gromacs using gcc 4.x that may cause this. see
a recent bugzilla entry about it.
Did you compile using the 4.x gcc? In that case, recompile with an
older version (3.x). That solution was suggested in the same
di
Hi,
First, our simulation system in physical world are mostly neutralized instead
of carrying charges. Second, there is requirement for PME for electrostatic
calculations. Neutralization is a not a must in 3.3.1 Gromacs; a background
charge will complement for the charges that system carries, b
Elias santos wrote:
Hi!!
I want know because we must neutralize the total load of the system
(protein + water) into of the box with genion.
You should neutralize the system and you also may want to add extra ions
to get up to physiological salt concentration.
--
What actually is it that you want to know about?
Your email doesn't really specify anything that you are trying to find out.
Are you wanting to maybe be able to neutralise the change in a system using
genion? Have you looked at the tutorials and checked "genion -h"?
-Original Message
Hi
yes I do use genion and g_rdf properly with 4.0.2
Regards
and
Sampo Karkola wrote:
> Hi,
>
> so you got genion working with 4.0.2?
>
> Sampo
>
> andrea spitaleri wrote:
>> gcc-4.0.2 seems ok for gmx-3.3.1
>> I have also submitted in bugzilla a similar problem with g_rdf
>>
>>
>> Regards
>>
Hi,
so you got genion working with 4.0.2?
Sampo
andrea spitaleri wrote:
gcc-4.0.2 seems ok for gmx-3.3.1
I have also submitted in bugzilla a similar problem with g_rdf
Regards
andrea
Sampo Karkola wrote:
Hi,
the same one, gcc-4.1. Have you tried with other versions?
Sampo
andrea spital
gcc-4.0.2 seems ok for gmx-3.3.1
I have also submitted in bugzilla a similar problem with g_rdf
Regards
andrea
Sampo Karkola wrote:
> Hi,
>
> the same one, gcc-4.1. Have you tried with other versions?
>
> Sampo
>
> andrea spitaleri wrote:
>> Hi
>> which gcc have you used for compiling gromac
Hi,
the same one, gcc-4.1. Have you tried with other versions?
Sampo
andrea spitaleri wrote:
Hi
which gcc have you used for compiling gromacs? I have the same problem in one
pc in which I have
build gromacs using gcc-4.1
Regards
andrea
Sampo Karkola wrote:
Dear list,
the genion program g
Hi
which gcc have you used for compiling gromacs? I have the same problem in one
pc in which I have
build gromacs using gcc-4.1
Regards
andrea
Sampo Karkola wrote:
> Dear list,
>
> the genion program gets halted when I'm trying to replace the solvent
> molecules with ions. The command
>
> gen
Maybe you forgot to delete the waters that were removed in the
ionization process?
/Pär
> Dear users:
> I want to prepare protein simulation on 0.15mol/l salt
> concentration,I use
> genion command to add ions,After genion,I change cln.top file last
> line to NA+
> 61,CL- 41.
>When I
Hi Zhong,
It seems that you are not using the correct .top file. Once you finish
adding ions with genion, you will need to generate
a new topology, which also contains ions.
Ciao,
Luciano
Dr. Luciano Triguero
College of Art and Science
Department of Chemistry
Cox Science Building
1301 Memoria
On 2/28/2007 7:52 PM, Mark Abraham wrote:
Qiang Zhong wrote:
Dear users:
I want to prepare protein simulation on 0.15mol/l salt
concentration,I use
genion command to add ions,After genion,I change cln.top file last
line to NA+
61,CL- 41.
When I execute grompp ,there are warning :
War
Qiang Zhong wrote:
Dear users:
I want to prepare protein simulation on 0.15mol/l salt concentration,I use
genion command to add ions,After genion,I change cln.top file last line to NA+
61,CL- 41.
When I execute grompp ,there are warning :
Warning: atom names in cln.top and cln_b4em.gro d
Something seems wrong with your topology. It seems grompp gets
confused about CL in one file being Na in the other. Maybe you added
the last lines to cln.top in the wrong order. It doesn't necessarily
cause the LINCS error later on, but suggests that your topology may
need some more work.
> Hi Guys,
>
>
>
> I have a question. I am using genion to add two ZN2+ ions to a protein
> that
> already has two. I thought I would just use genion with np 2. However
> it
> seemed to recognize that there were already two in the file and added
> none.
> So instead I used the parameter np 4.
Hi,
The error message tries to make clear that genion can only replace
water molecules in an index group without gaps. It has to be
continuous. So the point that was made earlier on the list was that
the water molecules should be deleted in the .gro file. Alternatively,
they can also be moved to
you might have deleted just one atom of water molecule.
Ex: If you are using SPC water , you have to delete all 3 atoms in index file.
Best way is to make changes in .gro file..
Renumber the resulting .gro file using genconf, make a new index file and start running.
On 10/10/06, Una Bjarnadott
> Dear Users,
>
> I'm hoping for an answear on my problem with neutralizing my system
adding
> 3 Cl ions with genion. When
> running grompp after genion with the new generated .gro file I get this
error:
>
> Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1)
Read closely - "T-Coupli
Una Bjarnadottir wrote:
Dear Users,
I'm hoping for an answear on my problem with neutralizing my system
adding 3 Cl ions with genion. When running grompp after genion with the
new generated .gro file I get this error:
Fatal error: Atom 33000 in multiple T-Coupling groups (15 and 1)
which i
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
>
>> You can try -norandom. I was under the impression that the potential
>> based placement was broken (had been for a while).
>
>
Hi David,
Thank you very much, the command line option -norandom did work and
placed the cations in the same place as
Miguel Ortiz Lombardia wrote:
-BEGIN PGP SIGNED MESSAGE-
Hash: SHA1
Dear colleagues,
It looks like genion behaviour has changed in gromacs 3.3.1 as compared
to 3.3
I still have both binaries in my machine and when using identical inputs
to add some Na cations the new one (3.3.1) adds t
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