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
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.
The command I entered in this step was:
genion -s protein_w.tpr -o protein_solv.gro -conc 0.15 -neutral -pname NA+
-nname CL-
How c
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
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 of file
'topol.top'
I checked the topol.
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
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 the system of pure 108 water molecules.But on running the
command genion I get error message
Processing topology
Back Off! I just backed up topol.top to ./#top
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
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 the genion.log file, it shows that th
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
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 filled_box.pdb -p
protein_mod_filled5.top -o ions
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
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 should normally be an integer. See
http://www.gromacs.org/Docum
Dear All,
I need to add 6 CL ions to make the system neutral but when I type the
command line
genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -nn 6
I am able to add the ion easily to a protein or protein-peptide complex by
using the above command line where I replace
Dear All,
I need to add 6 CL ions to make the system neutral but when I type the
command line
genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -nn 6
I am able to add the ion easily to a protein or protein-peptide complex by
using the above command line where I replace
Dear All,
I need to add 6 CL ions to make the system neutral but when I type the
command line
genion -s ions.tpr -o solv_ions.gro -p topol.top -pname NA -nname CL -nn 6
and choose group 15 (SOL), the error is
Fatal error:
No line with moleculetype 'SOL' found the [ molecules ] section of fi
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
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, i.e. 52 Mg ions
instead of 26 which wou
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
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 not a multiple of 19.
How to
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
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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
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 feedback says there is no Na (sodium) moleculetype.
I
Hi,
When using versions 4.5.2 and 4.5.3, I have noticed that genion now outputs a
file called "genion.log" (or "genion_node0.log" with 4.5.2) that appears to
contain the header information normally found in an md.log file produced by
mdrun (see below). Is this normal? There really isn't any
Hi List,
I was just wondering what is the relationship between the molarity and
the number of molecules. I have a system with 20 atoms of ligand, 761
water molecules, the box volume of 2.86 nanometer cube. I added 0.5 M
NaCl salt concentration using genion. I need to add. Genion put 7 Na+
and 7 Cl
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
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.gro -p top.top -o pr.tpr
i got a
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
I am simulating an ion channel and require help placing a concentration of
ions at one side of the box (below the membrane).
SETUP: membrane + embedded protein in the center of the cube.
I tried to generate a smaller cube (of the required volume below the cube),
solvate, add ions and then *cat* w
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
dear mark
my object is neutralization of system. please guide more
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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
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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
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Please
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
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.
This is not a big problem , but it looks is a l
Hi all,
I have a few probIems/confusions and will be extremely thankful for any
help. I added some "Cl- ions" by replacing water using "genion (and -nn)".
It generated a "topol.top" file with Cl listed in [ molecules ]. Now when I
try to run grompp, it gives an error saying "no such molecule type
Hi all,
I'm experiencing a strange problem with genion that I have never seen before. I
am preparing some membrane systems, many of which involve a large number of
charged lipids (several hundred). When using lipids with PC headgroups (no net
charge), the following works fine:
genion -s i
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,
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:
Program g
Dear all
I have added the new AMBER ion definitions from Joung and Cheatham to
my ffamber* force field files. Following the nomenclature these ions
have in AMBER, I use the same name for the atom name, the residue
name, and the molecule type, which includes the charge. E.g., I have
In ion
I sent the same message already yesterday but it doesn't seem to have
come through. Sorry if it did, and it was just me who for whatever
reason didn't get it.
Dear all
I have added the new AMBER ion definitions from Joung and Cheatham to
my ffamber* force field files. Following the nomenc
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
Dear justin
thanks for reply about g_dist.
about genion for peptides.Do I must use command genion for MD
peptides with one charge(13 aa)?Is it necessary for md?
best
sh-karbalaee
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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
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 water molecules with 200 Na+ GROMAC
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
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 any help.
Thanks,
Narayan
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
Dear all,
I am having problem with genion.
I have already search the gmx archive, and got the following message:
While using genion with -np 3, i get 2 lines of Replacing sol. xxx with Na and
it hangs up. With -np 1 it works fine and replaces 1 SOL with Na. I thought it
might be my system, so
list. It is not easy to get to know what you are asking.
Regards,
Yang Ye
- Original Message
From: Elias santos <[EMAIL PROTECTED]>
To: gmx-users
Sent: Tuesday, June 12, 2007 1:34:39 AM
Subject: [gmx-users] genion
Hi!!
I want know because we must neutralize the total load
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.
--
Hi!!
I want know because we must neutralize the total load of the system (protein
+ water) into of the box with genion.
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riginal Message-
From: [EMAIL PROTECTED] on behalf of Elias santos
Sent: Sun 6/10/2007 4:21 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] genion
Hi!!
I want know because we must neutralize the total load of the system (protein
+ water) in the interior of the box wit
Hi!!
I want know because we must neutralize the total load of the system (protein
+ water) in the interior of the box with genion.
Elias
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Please search t
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
Dear list,
the genion program gets halted when I'm trying to replace the solvent
molecules with ions. The command
genion -s protein_in_waterbox.tpr -o protein_out.gro -p topology.top
-pname NA+ -nname CL- -random -neutral -conc 0.1
asks for the group of solvent molecules and when I tell him
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
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-Original Message-
From: [EMAIL PROTECTED] on behalf of Qiang Zhong
Sent: Wed 2/28/2007 3:23 AM
To: gmx-users@gromacs.org
Subject: [gmx-users] genion error!
Dear users:
I want
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.
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 don't match (CL - Na)
> 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 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. This seemed to a
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,
In some of my simulations after neutralizing the systems with genion 2
of the ions were inside the active site cleft of the protein.
In the discussion on the list it was commented to either delete the
solvent within the protein which I did I deleted the water molecule
(11798) and
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