Re: [gmx-users] Genion error

[Justin Lemkul]

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 the command will simply 
fail.  You need to be replacing solvent molecules (usually water).  Please 
consult some basic tutorial material; such selections are always covered.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

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Re: [gmx-users] Genion error

[felipe vasquez]

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
Instituto Nacional de Salud
Avenida calle 26 No. 51-20 - Zona 6 CAN
Bogotá, D.C., Colombia


2013/10/24 Justin Lemkul 

>
>
> 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 was:
>>
>> genion -s protein_w.tpr -o protein_solv.gro -conc 0.15 -neutral -pname NA+
>> -nname CL-
>>
>>
> Depending on your Gromacs version, this command may not be right.  Ion
> names were changed as of version 4.5.
>
> -Justin
>
> --
> ==**
>
> Justin A. Lemkul, Ph.D.
> Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 601
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul@outerbanks.umaryland.**edu  | 
> (410)
> 706-7441
>
> ==**
> --
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Re: [gmx-users] Genion error

[Justin Lemkul]

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 was:

genion -s protein_w.tpr -o protein_solv.gro -conc 0.15 -neutral -pname NA+
-nname CL-



Depending on your Gromacs version, this command may not be right.  Ion names 
were changed as of version 4.5.


-Justin

--
==

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441

==
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Re: [[gmx-users] genion error!]

[Pär Bjelkmar]

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 execute grompp ,there are warning :
>
> Warning: atom names in cln.top and cln_b4em.gro don't match (CL - Na)
> 
> (more than 20 non-matching atom names)
> WARNING 1 [file "cln.top", line 9059]:
>   102 non-matching atom names
>   atom names from cln.top will be used
>   atom names from cln_b4em.gro will be ignored
>
> I continue to execute "mdrun nice 0 -v -s cln_em.tpr -o  
> minim_traj.trr -c
> minimized.gro -e minim_ener.edr",There are some error:
> Fatal error:
> Too many LINCS warnings (10190) - aborting to avoid logfile runaway.
> This normally happens when your system is not sufficiently  
> equilibrated,or if you
> are changing lambda too fast in free energy simulations.
> If you know what you are doing you can adjust the lincs warning  
> threshold
> in your mdp file, but normally it is better to fix the problem.
>
>  I don't know what happen ,could somebody tell me?
>   Thank you very much!
>
>
>
> pdb2gmx -f 4cln.pdb -o cln.gro -p cln.top
> editconf -f cln.gro -o cln.gro -bt octahedron -c -d 0.75
> genbox -cp cln.gro -cs spc216.gro -o cln_b4ion.gro -p cln.top
> grompp -f minim.mdp -c cln_b4ion.gro -p cln.top -o cln_b4ion.tpr
> genion -s cln_b4ion.tpr -o cln_b4em.gro -conc 0.15 -neutral
> grompp -f minim.mdp -c cln_b4em.gro -p cln.top -o cln_em.tpr
> mdrun -nice 0 -v -s cln_em.tpr -o minim_traj.trr -c minimized.gro -e
> minim_ener.edr
> grompp -f fullmd_sol.mdp -c minimized.gro -p cln.top -o fullmd.tpr
> mdrun -nice 0 -v -s fullmd.tpr -o md_traj.trr -x md_traj.xtc -c  
> md_final.gro -e
> md_ener.edr
>
>
>
>
> --
> Qiang Zhong
> Key Lab of Agricultural Animal Genetics, Breeding and Reproduction  
> of Ministry of Education
> College of Animal Sciences and Technology
> Huazhong Agricultural University
> Wuhan,Hubei, 430070
> PR China
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-- 
*
Pär BjelkmarStockholm Center for Biomembrane Research
Tel: +46-8-16 2746  Dep of Biochemistry and Biophysics
Fax: +46-8-15 3679  Stockholm University
[EMAIL PROTECTED]  10691 Stockholm, Sweden
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RE: [gmx-users] genion error!

[Triguero, Luciano O]

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 Memorial Drive, Room 146
P.O Box 249118
Coral Gables, FL 33124-0431
Cellular: 305-904-2419
Office: 305-284-3938



-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 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)

(more than 20 non-matching atom names)
WARNING 1 [file "cln.top", line 9059]:
  102 non-matching atom names
  atom names from cln.top will be used
  atom names from cln_b4em.gro will be ignored

I continue to execute "mdrun nice 0 -v -s cln_em.tpr -o minim_traj.trr -c
minimized.gro -e minim_ener.edr",There are some error:
Fatal error:
Too many LINCS warnings (10190) - aborting to avoid logfile runaway.
This normally happens when your system is not sufficiently equilibrated,or if 
you
are changing lambda too fast in free energy simulations.
If you know what you are doing you can adjust the lincs warning threshold
in your mdp file, but normally it is better to fix the problem.

 I don't know what happen ,could somebody tell me?
  Thank you very much!



pdb2gmx -f 4cln.pdb -o cln.gro -p cln.top
editconf -f cln.gro -o cln.gro -bt octahedron -c -d 0.75 
genbox -cp cln.gro -cs spc216.gro -o cln_b4ion.gro -p cln.top
grompp -f minim.mdp -c cln_b4ion.gro -p cln.top -o cln_b4ion.tpr
genion -s cln_b4ion.tpr -o cln_b4em.gro -conc 0.15 -neutral
grompp -f minim.mdp -c cln_b4em.gro -p cln.top -o cln_em.tpr
mdrun -nice 0 -v -s cln_em.tpr -o minim_traj.trr -c minimized.gro -e
minim_ener.edr
grompp -f fullmd_sol.mdp -c minimized.gro -p cln.top -o fullmd.tpr
mdrun -nice 0 -v -s fullmd.tpr -o md_traj.trr -x md_traj.xtc -c md_final.gro -e
md_ener.edr




--
Qiang Zhong
Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry 
of Education  
College of Animal Sciences and Technology 
Huazhong Agricultural University
Wuhan,Hubei, 430070
PR China
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Re: [gmx-users] genion error!

[Yang Ye]

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 :

Warning: atom names in cln.top and cln_b4em.gro don't match (CL - Na)

(more than 20 non-matching atom names)
WARNING 1 [file "cln.top", line 9059]:
  102 non-matching atom names
  atom names from cln.top will be used
  atom names from cln_b4em.gro will be ignored

I continue to execute "mdrun nice 0 -v -s cln_em.tpr -o 
minim_traj.trr -c

minimized.gro -e minim_ener.edr",There are some error:


Hardly surprising... most gromacs warnings should be considered 
carefully.
I think what Mark means is that in such case, you shall not continue to 
run mdrun without inspecting the warnings.
First the atom names in your .gro and .top files have to match those 
in the .atp files for the force field you're using. Then check the 
order and number of Na and Cl are correct.


Mark
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Re: [gmx-users] genion error!

[Mark Abraham]

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 don't match (CL - Na)

(more than 20 non-matching atom names)
WARNING 1 [file "cln.top", line 9059]:
  102 non-matching atom names
  atom names from cln.top will be used
  atom names from cln_b4em.gro will be ignored

I continue to execute "mdrun nice 0 -v -s cln_em.tpr -o minim_traj.trr -c
minimized.gro -e minim_ener.edr",There are some error:


Hardly surprising... most gromacs warnings should be considered carefully.

First the atom names in your .gro and .top files have to match those in 
the .atp files for the force field you're using. Then check the order 
and number of Na and Cl are correct.


Mark
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Re: [gmx-users] genion error!

[Erik Marklund]

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.


/Erik

28 feb 2007 kl. 09.23 skrev Qiang Zhong:


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)

(more than 20 non-matching atom names)
WARNING 1 [file "cln.top", line 9059]:
  102 non-matching atom names
  atom names from cln.top will be used
  atom names from cln_b4em.gro will be ignored

I continue to execute "mdrun nice 0 -v -s cln_em.tpr -o  
minim_traj.trr -c

minimized.gro -e minim_ener.edr",There are some error:
Fatal error:
Too many LINCS warnings (10190) - aborting to avoid logfile runaway.
This normally happens when your system is not sufficiently  
equilibrated,or if you

are changing lambda too fast in free energy simulations.
If you know what you are doing you can adjust the lincs warning  
threshold

in your mdp file, but normally it is better to fix the problem.

 I don't know what happen ,could somebody tell me?
  Thank you very much!



pdb2gmx -f 4cln.pdb -o cln.gro -p cln.top
editconf -f cln.gro -o cln.gro -bt octahedron -c -d 0.75
genbox -cp cln.gro -cs spc216.gro -o cln_b4ion.gro -p cln.top
grompp -f minim.mdp -c cln_b4ion.gro -p cln.top -o cln_b4ion.tpr
genion -s cln_b4ion.tpr -o cln_b4em.gro -conc 0.15 -neutral
grompp -f minim.mdp -c cln_b4em.gro -p cln.top -o cln_em.tpr
mdrun -nice 0 -v -s cln_em.tpr -o minim_traj.trr -c minimized.gro -e
minim_ener.edr
grompp -f fullmd_sol.mdp -c minimized.gro -p cln.top -o fullmd.tpr
mdrun -nice 0 -v -s fullmd.tpr -o md_traj.trr -x md_traj.xtc -c  
md_final.gro -e

md_ener.edr




--
Qiang Zhong
Key Lab of Agricultural Animal Genetics, Breeding and Reproduction  
of Ministry of Education

College of Animal Sciences and Technology
Huazhong Agricultural University
Wuhan,Hubei, 430070
PR China
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___
Erik Marklund, PhD student
Laboratory of Molecular Biophysics,
Dept. of Cell and Molecular Biology, Uppsala University.
Husargatan 3, Box 596,  75124 Uppsala, Sweden
phone:  +46 18 471 4537 fax: +46 18 511 755
[EMAIL PROTECTED]   http://xray.bmc.uu.se/molbiophys


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