Re: Re: [gmx-users] total charge of the system

2011-01-25 Thread Mark Abraham 


On 01/25/11, ahmet yıldırım   wrote:
> Dear Mark,
> 
> A million thanks. Problem is solved. 
> Finally,
> Select a continuous group of solvent molecules:
> ...
> Group    12 (  Water) has 126219 elements
> Group    13 (    SOL) has 126219 elements
> 
> 
> Which one should I choose 12 or 13?
> 

They're probably the same.

Mark

> 
> 
> Final topol.top file:
> 
> 
> ;    File 'topol.top' was generated
> ;    By user: onbekend (0)
> ;    On host: onbekend
> ;    At date: Tue Jan 25 10:12:14 2011
> 
> ;
> ;    This is a standalone topology file
> ;
> ;    It was generated using program:
> ;    pdb2gmx - VERSION 4.5.3
> ;
> ;    Command line was:
> ;    pdb2gmx -f 3MOA.pdb -water spc -ter 
> ;
> ;    Force field was read from the standard Gromacs share directory.
> 
> ;
> 
> ; Include forcefield parameters
> #include "gromos43a1.ff/forcefield.itp"
> 
> ; Include chain topologies
> #include "topol_Protein_chain_P.itp"
> #include "topol_Protein_chain_L.itp"
> 
> #include "topol_Protein_chain_H.itp"
> 
> ; Include water topology
> #include "gromos43a1.ff/spc.itp"
> 
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> 
> ;  i funct   fcx    fcy    fcz
>    1    1   1000   1000   1000
> #endif
> 
> ; Include topology for ions
> #include "gromos43a1.ff/ions.itp"
> 
> [ system ]
> ; Name
> GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 
> ANTIBODY 2F5 HEAVY CHAIN in water
> 
> 
> [ molecules ]
> ; Compound    #mols
> Protein_chain_P 1
> Protein_chain_L 1
> Protein_chain_H 1
> SOL    10
> SOL   127
> SOL   157
> SOL 41771
> 
> CL         8
> 
> 
> 
> 25 Ocak 2011 13:13 tarihinde Mark Abraham  yazdı:
> 
> > 
> > 
> > 
> > On 01/25/11, ahmet yıldırım   wrote:
> > 
> > > 
> > > Dear Mark and Emanuel,
> > > 
> > > I am sending the ions.tip and the topol.top files. Everything seems ok. 
> > > Any problem about these files?
> > > 
> > > 
> > 
> > 
> > No. So one of the other #include files is erroneously defining ion molecule 
> > types. See 
> > www.gromacs.org/Documentation/Include_File_Mechanism(http://www.gromacs.org/Documentation/Include_File_Mechanism).
> >  Go and read them and fix it.
> > 
> > 
> > As the link I sent last time hinted, you need to name *molecules* in the 
> > [molecules] directive. Look carefully at the *molecule* name of chloride 
> > where it is defined.
> > 
> > Mark
> > 
> > 
> > 
> > > 
> > > 
> > > 
> > > By the way, I am using the Gromacs 4.5.3.
> > > Force Field 43a1
> > > 
> > > 25 Ocak 2011 12:03 tarihinde Emanuel Peter 
> > >  yazdı:
> > > 
> > > 
> > > 
> > > > Hello,
> > > > 
> > > > You have to look into your ions.itp which is included in your top-file 
> > > > by #include ions.itp.
> > > > 
> > > > 
> > > > There all the types of ions have to be defined.
> > > > The atom-types which you can see in the ions.itp, you will
> > > > find in the ff"your-forcefield".itp where your atomtypes are defined.
> > > > On top of your .top file the Atomtype-itp-file is included.
> > > > 
> > > > 
> > > > All these files are normally placed in /usr/share/gromacs/top/.
> > > > But you also can place them into your current directory.
> > > > 
> > > > Bests,
> > > > 
> > > > Emanuel
> > > > 
> > > > >>> Mark Abraham  25.01.11 10.48 Uhr >>>
> > > > 
> > > > 
> > > > 
> > > > 
> > > > 
> > > > 
> > > > 
> > > > On 01/25/11, ahmet yıldırım   wrote:
> > > > > 
> > > > > 
> > > > > Dear Mark,
> > > > > 
> > > > > I looked at gromacs mail list but I could not find a proper solution 
> > > > > .What should I add to the .top file? Please look at the following 
> > > > > reconstructed1 .top and reconstructed1 .top files
> > > > > 
> > > > > 
> > > > > 
> > > > > 
> > > > > I have error as the following reconstructed1 .top file:
> > > > > 
> > > > > Fatal error:
> > > > > 
> > > > > moleculetype CU1 is redefined
> > > > > 
> > > > > 
> > > > > I have error as the following reconstructed2 .top file:
> > > > > 
> > > > > Fatal error:
> > > > > 
> > > > > No such moleculetype CL-
> > > > > 
> > > > > 
> > > > 
> > > > I don't have any knowledge of the context, so can't answer. It looks to 
> > > > me like you are mixing copies of ions.itp from multiple sources. Don't. 
> > > > Use the one for the force field you are targetting. pdb2gmx generated 
> > > > the right invocation - all you should have to do is use that by 
> > > > generating correctly-named ions. See 
> > > > http://www.gromacs.org/Documentation/Gromacs_Utilities/genion(http://www.gromacs.org/Documentation/Gromacs_Utilities/genion)
> > > > 
> > > > 
> > > > 
> > > > Mark
> > > > 
> > > > 
> > > > > Original .top file:
> > > > > ; Include topology for ions
> > > > > #include "gromos43a1.ff/ions.itp"
> > > > > 
> > > > > 
> > > > > 
> > > > > [ system ]
> > > > > ; Name
> > > > > GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; 
> > > > > ANTI-HIV-1 ANTIBODY 2F5

Re: Re: [gmx-users] total charge of the system

2011-01-25 Thread ahmet yıldırım 
Dear Mark,

A million thanks. Problem is solved.
Finally,
Select a continuous group of solvent molecules:
...
Group12 (  Water) has 126219 elements
Group13 (SOL) has 126219 elements

Which one should I choose 12 or 13?

*Final topol.top file:


*;File 'topol.top' was generated
;By user: onbekend (0)
;On host: onbekend
;At date: Tue Jan 25 10:12:14 2011
;
;This is a standalone topology file
;
;It was generated using program:
;pdb2gmx - VERSION 4.5.3
;
;Command line was:
;pdb2gmx -f 3MOA.pdb -water spc -ter
;
;Force field was read from the standard Gromacs share directory.
;

; Include forcefield parameters
#include "gromos43a1.ff/forcefield.itp"

; Include chain topologies
#include "topol_Protein_chain_P.itp"
#include "topol_Protein_chain_L.itp"
#include "topol_Protein_chain_H.itp"

; Include water topology
#include "gromos43a1.ff/spc.itp"

#ifdef POSRES_WATER
; Position restraint for each water oxygen
[ position_restraints ]
;  i funct   fcxfcyfcz
   11   1000   1000   1000
#endif

; Include topology for ions
#include "gromos43a1.ff/ions.itp"

[ system ]
; Name
GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1
ANTIBODY 2F5 HEAVY CHAIN in water

[ molecules ]
; Compound#mols
Protein_chain_P 1
Protein_chain_L 1
Protein_chain_H 1
SOL10
SOL   127
SOL   157
SOL 41771
*CL 8
*


25 Ocak 2011 13:13 tarihinde Mark Abraham  yazdı:

>
>
> On 01/25/11, *ahmet yıldırım *  wrote:
>
> Dear Mark and Emanuel,
>
> I am sending the ions.tip and the topol.top files. Everything seems ok. Any
> problem about these files?
>
>
> No. So one of the other #include files is erroneously defining ion molecule
> types. See www.gromacs.org/Documentation/Include_File_Mechanism. Go and
> read them and fix it.
>
> As the link I sent last time hinted, you need to name *molecules* in the
> [molecules] directive. Look carefully at the *molecule* name of chloride
> where it is defined.
>
> Mark
>
>
>
> By the way, I am using the Gromacs 4.5.3.
> Force Field 43a1
>
> 25 Ocak 2011 12:03 tarihinde Emanuel Peter <
> emanuel.pe...@chemie.uni-regensburg.de> yazdı:
>
>> Hello,
>>
>> You have to look into your ions.itp which is included in your top-file by
>> #include ions.itp.
>> There all the types of ions have to be defined.
>> The atom-types which you can see in the ions.itp, you will
>> find in the ff"your-forcefield".itp where your atomtypes are defined.
>> On top of your .top file the Atomtype-itp-file is included.
>> All these files are normally placed in /usr/share/gromacs/top/.
>> But you also can place them into your current directory.
>>
>> Bests,
>>
>> Emanuel
>>
>> >>> Mark Abraham 25.01.11 10.48 Uhr >>>
>>
>>
>>
>>
>> On 01/25/11, *ahmet yıldırım *  wrote:
>>
>> Dear Mark,
>>
>> I looked at gromacs mail list but I could not find a proper solution .
>> What should I add to the .top file? Please look at the following
>> reconstructed1 .top and reconstructed1 .top files
>>
>> I have error as the following reconstructed1 .top file:
>> *Fatal error:*
>> moleculetype CU1 is redefined
>>
>> I have error as the following reconstructed2 .top file:
>> *Fatal error:*
>> No such moleculetype CL-
>> **
>>
>>
>> I don't have any knowledge of the context, so can't answer. It looks to me
>> like you are mixing copies of ions.itp from multiple sources. Don't. Use the
>> one for the force field you are targetting. pdb2gmx generated the right
>> invocation - all you should have to do is use that by generating
>> correctly-named ions. 
>> Seehttp://www.gromacs.org/Documentation/Gromacs_Utilities/genion
>>
>> Mark
>>
>> *Original .top file:*
>> ; Include topology for ions
>> #include "gromos43a1.ff/ions.itp"
>>
>> [ system ]
>> ; Name
>> GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1
>> ANTIBODY 2F5 HEAVY CHAIN in water
>>
>> [ molecules ]
>> ; Compound#mols
>> Protein_chain_P 1
>> Protein_chain_L 1
>> Protein_chain_H 1
>> SOL10
>> SOL   127
>> SOL   157
>> SOL 41779
>>
>> *reconstructed1 .top file*
>> ; Include topology for ions
>> #include "gromos43a1.ff/ions.itp"
>> *#include "ions.itp"*
>>
>> [ system ]
>> ; Name
>> GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1
>> ANTIBODY 2F5 HEAVY CHAIN in water
>>
>> [ molecules ]
>> ; Compound#mols
>> Protein_chain_P 1
>> Protein_chain_L 1
>> Protein_chain_H 1
>> SOL10
>> SOL   127
>> SOL   157
>> SOL 4177*1*
>> CL-   *8*
>> *reconstructed2 .top file*
>> ; Include topology for ions
>> #include "gromos43a1.ff/ions.itp"
>> **
>> [ system ]
>> ; Name
>> GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1
>> ANTIBODY 2F5 HEAVY CHAIN in water
>>
>> [ molecules ]
>> ; Compou

Re: Re: [gmx-users] total charge of the system

2011-01-25 Thread Mark Abraham 


On 01/25/11, ahmet yıldırım   wrote:
> Dear Mark and Emanuel,
> 
> I am sending the ions.tip and the topol.top files. Everything seems ok. Any 
> problem about these files?
> 

No. So one of the other #include files is erroneously defining ion molecule 
types. See www.gromacs.org/Documentation/Include_File_Mechanism. Go and read 
them and fix it.

As the link I sent last time hinted, you need to name *molecules* in the 
[molecules] directive. Look carefully at the *molecule* name of chloride where 
it is defined.

Mark

> 
> 
> 
> By the way, I am using the Gromacs 4.5.3.
> Force Field 43a1
> 
> 25 Ocak 2011 12:03 tarihinde Emanuel Peter 
>  yazdı:
> 
> 
> > Hello,
> > 
> > You have to look into your ions.itp which is included in your top-file by 
> > #include ions.itp.
> > 
> > There all the types of ions have to be defined.
> > The atom-types which you can see in the ions.itp, you will
> > find in the ff"your-forcefield".itp where your atomtypes are defined.
> > On top of your .top file the Atomtype-itp-file is included.
> > 
> > All these files are normally placed in /usr/share/gromacs/top/.
> > But you also can place them into your current directory.
> > 
> > Bests,
> > 
> > Emanuel
> > 
> > >>> Mark Abraham  25.01.11 10.48 Uhr >>>
> > 
> > 
> > 
> > 
> > 
> > On 01/25/11, ahmet yıldırım   wrote:
> > > 
> > > Dear Mark,
> > > 
> > > I looked at gromacs mail list but I could not find a proper solution 
> > > .What should I add to the .top file? Please look at the following 
> > > reconstructed1 .top and reconstructed1 .top files
> > > 
> > > 
> > > 
> > > I have error as the following reconstructed1 .top file:
> > > 
> > > Fatal error:
> > > 
> > > moleculetype CU1 is redefined
> > > 
> > > 
> > > I have error as the following reconstructed2 .top file:
> > > 
> > > Fatal error:
> > > 
> > > No such moleculetype CL-
> > > 
> > > 
> > 
> > I don't have any knowledge of the context, so can't answer. It looks to me 
> > like you are mixing copies of ions.itp from multiple sources. Don't. Use 
> > the one for the force field you are targetting. pdb2gmx generated the right 
> > invocation - all you should have to do is use that by generating 
> > correctly-named ions. See 
> > http://www.gromacs.org/Documentation/Gromacs_Utilities/genion(http://www.gromacs.org/Documentation/Gromacs_Utilities/genion)
> > 
> > 
> > Mark
> > 
> > 
> > > Original .top file:
> > > ; Include topology for ions
> > > #include "gromos43a1.ff/ions.itp"
> > > 
> > > 
> > > [ system ]
> > > ; Name
> > > GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; 
> > > ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water
> > > 
> > > 
> > > [ molecules ]
> > > ; Compound    #mols
> > > Protein_chain_P 1
> > > Protein_chain_L 1
> > > Protein_chain_H 1
> > > SOL    10
> > > SOL   127
> > > SOL   157
> > > SOL 41779
> > > 
> > > 
> > > 
> > > reconstructed1 .top file
> > > ; Include topology for ions
> > > #include "gromos43a1.ff/ions.itp"
> > > #include "ions.itp"
> > > 
> > > [ system ]
> > > ; Name
> > > GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; 
> > > ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water
> > > 
> > > 
> > > 
> > > [ molecules ]
> > > ; Compound    #mols
> > > Protein_chain_P 1
> > > Protein_chain_L 1
> > > Protein_chain_H 1
> > > SOL    10
> > > SOL   127
> > > SOL   157
> > > SOL 41771
> > > 
> > > 
> > > CL-           8
> > > reconstructed2 .top file
> > > ; Include topology for ions
> > > #include "gromos43a1.ff/ions.itp"
> > > 
> > > [ system ]
> > > ; Name
> > > GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; 
> > > ANTI-HIV-1 ANTIBODY 2F5 HEAVY CHAIN in water
> > > 
> > > 
> > > 
> > > [ molecules ]
> > > ; Compound    #mols
> > > Protein_chain_P 1
> > > Protein_chain_L 1
> > > Protein_chain_H 1
> > > SOL    10
> > > SOL   127
> > > SOL   157
> > > SOL 41771
> > > 
> > > 
> > > CL-           8
> > > 
> > > 
> > > 25 Ocak 2011 10:49 tarihinde Mark Abraham  yazdı:
> > > 
> > > 
> > > > 
> > > > 
> > > > 
> > > > On 01/25/11, ahmet yıldırım   wrote:
> > > > > 
> > > > > 
> > > > > Hi,
> > > > > 
> > > > > In my simulation, total charge of the system is a noninteger number 
> > > > > (System has non-zero total charge: 8.04e+00). I neutralized it 
> > > > > with 8 chlorine atoms. 
> > > > > Then, grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
> > > > > 
> > > > > 
> > > > > 
> > > > > 
> > > > > Fatal error:
> > > > > 
> > > > > moleculetype CU1 is redefined
> > > > > is it some thing wrong?
> > > > > 
> > > > 
> > > > 
> > > > ions.itp defines molecule types for ions. Molecule types cannot be 
> > > > redefined. When you #included ions.itp GROMACS thought you were doing 
> > > > illegal redefinitions. Look back in the .top to find the original 
> > > > definitions, and then

Re: Re: [gmx-users] total charge of the system

2011-01-25 Thread ahmet yıldırım 
Dear Mark and Emanuel,

I am sending the ions.tip and the topol.top files. Everything seems ok. Any
problem about these files?

By the way, I am using the Gromacs 4.5.3.
Force Field 43a1

25 Ocak 2011 12:03 tarihinde Emanuel Peter <
emanuel.pe...@chemie.uni-regensburg.de> yazdı:

> Hello,
>
> You have to look into your ions.itp which is included in your top-file by
> #include ions.itp.
> There all the types of ions have to be defined.
> The atom-types which you can see in the ions.itp, you will
> find in the ff"your-forcefield".itp where your atomtypes are defined.
> On top of your .top file the Atomtype-itp-file is included.
> All these files are normally placed in /usr/share/gromacs/top/.
> But you also can place them into your current directory.
>
> Bests,
>
> Emanuel
>
> >>> Mark Abraham 25.01.11 10.48 Uhr >>>
>
>
>
> On 01/25/11, *ahmet yıldırım *  wrote:
>
> Dear Mark,
>
> I looked at gromacs mail list but I could not find a proper solution 
> .Whatshould
> I add to the .top file? Please look at the following reconstructed1 .top
> and reconstructed1 .top files
>
> I have error as the following reconstructed1 .top file:
> *Fatal error:*
> moleculetype CU1 is redefined
>
> I have error as the following reconstructed2 .top file:
> *Fatal error:*
> No such moleculetype CL-
> **
>
>
> I don't have any knowledge of the context, so can't answer. It looks to me
> like you are mixing copies of ions.itp from multiple sources. Don't. Use the
> one for the force field you are targetting. pdb2gmx generated the right
> invocation - all you should have to do is use that by generating
> correctly-named ions. 
> Seehttp://www.gromacs.org/Documentation/Gromacs_Utilities/genion
>
> Mark
>
> *Original .top file:*
> ; Include topology for ions
> #include "gromos43a1.ff/ions.itp"
>
> [ system ]
> ; Name
> GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1
> ANTIBODY 2F5 HEAVY CHAIN in water
>
> [ molecules ]
> ; Compound#mols
> Protein_chain_P 1
> Protein_chain_L 1
> Protein_chain_H 1
> SOL10
> SOL   127
> SOL   157
> SOL 41779
>
> *reconstructed1 .top file*
> ; Include topology for ions
> #include "gromos43a1.ff/ions.itp"
> *#include "ions.itp"*
>
> [ system ]
> ; Name
> GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1
> ANTIBODY 2F5 HEAVY CHAIN in water
>
> [ molecules ]
> ; Compound#mols
> Protein_chain_P 1
> Protein_chain_L 1
> Protein_chain_H 1
> SOL10
> SOL   127
> SOL   157
> SOL 4177*1*
> CL-   *8*
> *reconstructed2 .top file*
> ; Include topology for ions
> #include "gromos43a1.ff/ions.itp"
> **
> [ system ]
> ; Name
> GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1
> ANTIBODY 2F5 HEAVY CHAIN in water
>
> [ molecules ]
> ; Compound#mols
> Protein_chain_P 1
> Protein_chain_L 1
> Protein_chain_H 1
> SOL10
> SOL   127
> SOL   157
> SOL 4177*1*
> CL-   *8*
>
>
> 25 Ocak 2011 10:49 tarihinde Mark Abraham  yazdı:
>
>>
>>
>> On 01/25/11, *ahmet yıldırım *  wrote:
>>
>> Hi,
>>
>> In my simulation, total charge of the system is a noninteger number
>> (System has non-zero total charge: 8.04e+00). I neutralized it with 8
>> chlorine atoms.
>> Then, grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
>>
>> Fatal error:
>> moleculetype CU1 is redefined
>> is it some thing wrong?
>>
>>
>> ions.itp defines molecule types for ions. Molecule types cannot be
>> redefined. When you #included ions.itp GROMACS thought you were doing
>> illegal redefinitions. Look back in the .top to find the original
>> definitions, and then take suitable action.
>>
>> Mark
>>
>>
>>
>>
>>
>> Below is the first and final version of the .top file:
>>
>> First topol.top File
>> **
>> [ molecules ]
>> ; Compound#mols
>> Protein_chain_P 1
>> Protein_chain_L  1
>> Protein_chain_H 1
>> SOL 10
>> SOL127
>> SOL157
>> SOL 41779
>> **
>>
>> Final topol.top File
>> *#include "ions.itp"*
>>
>> [ molecules ]
>> ; Compound#mols
>> Protein_chain_P 1
>> Protein_chain_L  1
>> Protein_chain_H 1
>> SOL 10
>> SOL127
>> SOL157
>> SOL *41771*
>> *CL- 8*
>>
>>
>>
>>
>>
>>
>> --
>> Ahmet YILDIRIM
>>
>>
>> --
>> gmx-users mailing listgmx-users@gromacs.org
>> http://lists.gromacs.org/mailman/listinfo/gmx-users
>> Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
>> Please don't post (un)subscribe requests to the list. Use the
>> www interface or send it to gmx-users-requ...@gromacs.org.
>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> Ahmet YILDIRIM

Antw: Re: [gmx-users] total charge of the system

2011-01-25 Thread Emanuel Peter 
Hello,

You have to look into your ions.itp which is included in your top-file by
#include ions.itp.
There all the types of ions have to be defined.
The atom-types which you can see in the ions.itp, you will
find in the ff"your-forcefield".itp where your atomtypes are defined.
On top of your .top file the Atomtype-itp-file is included.
All these files are normally placed in /usr/share/gromacs/top/.
But you also can place them into your current directory.

Bests,

Emanuel

>>> Mark Abraham  25.01.11 10.48 Uhr >>>


On 01/25/11, ahmet yıldırım   wrote:Dear Mark,

I looked at gromacs mail list but I could not find a proper solution .What
should I add to the .top file? Please look at the following reconstructed1 .top
and reconstructed1 .top files

I have error as the following reconstructed1 .top file:
Fatal error:
moleculetype CU1 is redefined

I have error as the following reconstructed2 .top file:
Fatal error:
No such moleculetype CL-


I don't have any knowledge of the context, so can't answer. It looks to me like
you are mixing copies of ions.itp from multiple sources. Don't. Use the one for
the force field you are targetting. pdb2gmx generated the right invocation -
all you should have to do is use that by generating correctly-named ions. See
http://www.gromacs.org/Documentation/Gromacs_Utilities/genion

Mark

Original .top file:
; Include topology for ions
#include "gromos43a1.ff/ions.itp"

[ system ]
; Name
GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1
ANTIBODY 2F5 HEAVY CHAIN in water

[ molecules ]
; Compound#mols
Protein_chain_P 1
Protein_chain_L 1
Protein_chain_H 1
SOL10
SOL   127
SOL   157
SOL 41779

reconstructed1 .top file
; Include topology for ions
#include "gromos43a1.ff/ions.itp"
#include "ions.itp"

[ system ]
; Name
GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1
ANTIBODY 2F5 HEAVY CHAIN in water

[ molecules ]
; Compound#mols
Protein_chain_P 1
Protein_chain_L 1
Protein_chain_H 1
SOL10
SOL   127
SOL   157
SOL 41771
CL-   8
reconstructed2 .top file
; Include topology for ions
#include "gromos43a1.ff/ions.itp"

[ system ]
; Name
GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1
ANTIBODY 2F5 HEAVY CHAIN in water

[ molecules ]
; Compound#mols
Protein_chain_P 1
Protein_chain_L 1
Protein_chain_H 1
SOL10
SOL   127
SOL   157
SOL 41771
CL-   8


25 Ocak 2011 10:49 tarihinde Mark Abraham  yazdı:


On 01/25/11, ahmet yıldırım   wrote:Hi,

In my simulation, total charge of the system is a noninteger number (System has
non-zero total charge: 8.04e+00). I neutralized it with 8 chlorine atoms. 
Then, grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr

Fatal error:
moleculetype CU1 is redefined
is it some thing wrong?


ions.itp defines molecule types for ions. Molecule types cannot be redefined.
When you #included ions.itp GROMACS thought you were doing illegal
redefinitions. Look back in the .top to find the original definitions, and then
take suitable action.

Mark





Below is the first and final version of the .top file:

First topol.top File

[ molecules ]
; Compound#mols
Protein_chain_P 1
Protein_chain_L  1
Protein_chain_H 1
SOL 10
SOL127
SOL157
SOL 41779


Final topol.top File
#include "ions.itp"

[ molecules ]
; Compound#mols
Protein_chain_P 1
Protein_chain_L  1
Protein_chain_H 1
SOL 10
SOL127
SOL157
SOL 41771
CL- 8






-- 
Ahmet YILDIRIM




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Re: [gmx-users] total charge of the system

2011-01-25 Thread Mark Abraham 


On 01/25/11, ahmet yıldırım   wrote:
> Dear Mark,
> 
> I looked at gromacs mail list but I could not find a proper solution .What 
> should I add to the .top file? Please look at the following reconstructed1 
> .top and reconstructed1 .top files
> 
> 
> I have error as the following reconstructed1 .top file:
> 
> Fatal error:
> 
> moleculetype CU1 is redefined
> 
> 
> I have error as the following reconstructed2 .top file:
> 
> Fatal error:
> 
> No such moleculetype CL-
> 
> 

I don't have any knowledge of the context, so can't answer. It looks to me like 
you are mixing copies of ions.itp from multiple sources. Don't. Use the one for 
the force field you are targetting. pdb2gmx generated the right invocation - 
all you should have to do is use that by generating correctly-named ions. See 
http://www.gromacs.org/Documentation/Gromacs_Utilities/genion(http://www.gromacs.org/Documentation/Gromacs_Utilities/genion)

Mark


> Original .top file:
> ; Include topology for ions
> #include "gromos43a1.ff/ions.itp"
> 
> [ system ]
> ; Name
> GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 
> ANTIBODY 2F5 HEAVY CHAIN in water
> 
> 
> [ molecules ]
> ; Compound    #mols
> Protein_chain_P 1
> Protein_chain_L 1
> Protein_chain_H 1
> SOL    10
> SOL   127
> SOL   157
> SOL 41779
> 
> 
> reconstructed1 .top file
> ; Include topology for ions
> #include "gromos43a1.ff/ions.itp"
> #include "ions.itp"
> 
> [ system ]
> ; Name
> GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 
> ANTIBODY 2F5 HEAVY CHAIN in water
> 
> 
> [ molecules ]
> ; Compound    #mols
> Protein_chain_P 1
> Protein_chain_L 1
> Protein_chain_H 1
> SOL    10
> SOL   127
> SOL   157
> SOL 41771
> 
> CL-           8
> reconstructed2 .top file
> ; Include topology for ions
> #include "gromos43a1.ff/ions.itp"
> 
> [ system ]
> ; Name
> GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1 
> ANTIBODY 2F5 HEAVY CHAIN in water
> 
> 
> [ molecules ]
> ; Compound    #mols
> Protein_chain_P 1
> Protein_chain_L 1
> Protein_chain_H 1
> SOL    10
> SOL   127
> SOL   157
> SOL 41771
> 
> CL-           8
> 
> 
> 25 Ocak 2011 10:49 tarihinde Mark Abraham  yazdı:
> 
> > 
> > 
> > 
> > On 01/25/11, ahmet yıldırım   wrote:
> > > 
> > > Hi,
> > > 
> > > In my simulation, total charge of the system is a noninteger number 
> > > (System has non-zero total charge: 8.04e+00). I neutralized it with 8 
> > > chlorine atoms. 
> > > Then, grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
> > > 
> > > 
> > > 
> > > Fatal error:
> > > 
> > > moleculetype CU1 is redefined
> > > is it some thing wrong?
> > > 
> > 
> > 
> > ions.itp defines molecule types for ions. Molecule types cannot be 
> > redefined. When you #included ions.itp GROMACS thought you were doing 
> > illegal redefinitions. Look back in the .top to find the original 
> > definitions, and then take suitable action.
> > 
> > 
> > Mark
> > 
> > 
> > 
> > > 
> > > 
> > > Below is the first and final version of the .top file:
> > > 
> > > 
> > > 
> > > First topol.top File
> > > 
> > > [ molecules ]
> > > ; Compound    #mols
> > > Protein_chain_P 1
> > > Protein_chain_L  1
> > > Protein_chain_H 1
> > > SOL 10
> > > SOL    127
> > > 
> > > 
> > > SOL        157
> > > SOL 41779
> > > 
> > > 
> > > Final topol.top File
> > > #include "ions.itp"
> > > 
> > > [ molecules ]
> > > ; Compound    #mols
> > > Protein_chain_P 1
> > > Protein_chain_L  1
> > > 
> > > 
> > > Protein_chain_H 1
> > > SOL 10
> > > SOL    127
> > > SOL        157
> > > SOL 41771
> > > CL-         8
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > 
> > > -- 
> > > Ahmet YILDIRIM
> > > 
> > > 
> > > 
> > 
> > 
> > 
> > 
> > --
> > 
> > gmx-users mailing list    gmx-users@gromacs.org
> > 
> > http://lists.gromacs.org/mailman/listinfo/gmx-users
> > 
> > Please search the archive at 
> > http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> > 
> > Please don't post (un)subscribe requests to the list. Use the
> > 
> > www interface or send it to gmx-users-requ...@gromacs.org.
> > 
> > Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
> > 
> 
> 
> 
> 
> -- 
> Ahmet YILDIRIM
> 
> 
>
-- 
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Re: [gmx-users] total charge of the system

2011-01-25 Thread ahmet yıldırım 
Dear Mark,

I looked at gromacs mail list but I could not find a proper solution
.Whatshould
I add to the .top file? Please look at the following reconstructed1 .top and
reconstructed1 .top files

I have error as the following reconstructed1 .top file:
*Fatal error:*
moleculetype CU1 is redefined

I have error as the following reconstructed2 .top file:
*Fatal error:*
No such moleculetype CL-
*
Original .top file:*
; Include topology for ions
#include "gromos43a1.ff/ions.itp"

[ system ]
; Name
GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1
ANTIBODY 2F5 HEAVY CHAIN in water

[ molecules ]
; Compound#mols
Protein_chain_P 1
Protein_chain_L 1
Protein_chain_H 1
SOL10
SOL   127
SOL   157
SOL 41779

*reconstructed1 .top file*
; Include topology for ions
#include "gromos43a1.ff/ions.itp"
*#include "ions.itp"*

[ system ]
; Name
GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1
ANTIBODY 2F5 HEAVY CHAIN in water

[ molecules ]
; Compound#mols
Protein_chain_P 1
Protein_chain_L 1
Protein_chain_H 1
SOL10
SOL   127
SOL   157
SOL 4177*1*
CL-   *8*
*reconstructed2 .top file*
; Include topology for ions
#include "gromos43a1.ff/ions.itp"
**
[ system ]
; Name
GP41 MPER-DERIVED PEPTIDE; ANTI-HIV-1 ANTIBODY 2F5 LIGHT CHAIN; ANTI-HIV-1
ANTIBODY 2F5 HEAVY CHAIN in water

[ molecules ]
; Compound#mols
Protein_chain_P 1
Protein_chain_L 1
Protein_chain_H 1
SOL10
SOL   127
SOL   157
SOL 4177*1*
CL-   *8*


25 Ocak 2011 10:49 tarihinde Mark Abraham  yazdı:

>
>
> On 01/25/11, *ahmet yıldırım *  wrote:
>
> Hi,
>
> In my simulation, total charge of the system is a noninteger number (System
> has non-zero total charge: 8.04e+00). I neutralized it with 8 chlorine
> atoms.
> Then, grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
>
> Fatal error:
> moleculetype CU1 is redefined
> is it some thing wrong?
>
>
> ions.itp defines molecule types for ions. Molecule types cannot be
> redefined. When you #included ions.itp GROMACS thought you were doing
> illegal redefinitions. Look back in the .top to find the original
> definitions, and then take suitable action.
>
> Mark
>
>
>
>
> Below is the first and final version of the .top file:
>
> First topol.top File
> **
> [ molecules ]
> ; Compound#mols
> Protein_chain_P 1
> Protein_chain_L  1
> Protein_chain_H 1
> SOL 10
> SOL127
> SOL157
> SOL 41779
> **
>
> Final topol.top File
> *#include "ions.itp"*
>
> [ molecules ]
> ; Compound#mols
> Protein_chain_P 1
> Protein_chain_L  1
> Protein_chain_H 1
> SOL 10
> SOL127
> SOL157
> SOL *41771*
> *CL- 8*
>
>
>
>
>
>
> --
> Ahmet YILDIRIM
>
>
> --
> gmx-users mailing listgmx-users@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at
> http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
> Please don't post (un)subscribe requests to the list. Use the
> www interface or send it to gmx-users-requ...@gromacs.org.
> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>



-- 
Ahmet YILDIRIM
-- 
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Re: [gmx-users] total charge of the system

2011-01-25 Thread Mark Abraham 


On 01/25/11, ahmet yıldırım   wrote:
> Hi,
> 
> In my simulation, total charge of the system is a noninteger number (System 
> has non-zero total charge: 8.04e+00). I neutralized it with 8 chlorine 
> atoms. 
> Then, grompp -f em.mdp -p topol.top -c solvated.gro -o em.tpr
> 
> 
> Fatal error:
> 
> moleculetype CU1 is redefined
> is it some thing wrong?
> 

ions.itp defines molecule types for ions. Molecule types cannot be redefined. 
When you #included ions.itp GROMACS thought you were doing illegal 
redefinitions. Look back in the .top to find the original definitions, and then 
take suitable action.

Mark


> 
> 
> Below is the first and final version of the .top file:
> 
> 
> First topol.top File
> 
> [ molecules ]
> ; Compound    #mols
> Protein_chain_P 1
> Protein_chain_L  1
> Protein_chain_H 1
> SOL 10
> SOL    127
> 
> SOL        157
> SOL 41779
> 
> 
> Final topol.top File
> #include "ions.itp"
> 
> [ molecules ]
> ; Compound    #mols
> Protein_chain_P 1
> Protein_chain_L  1
> 
> Protein_chain_H 1
> SOL 10
> SOL    127
> SOL        157
> SOL 41771
> CL-         8
> 
> 
> 
> 
> 
> 
> 
> -- 
> Ahmet YILDIRIM
> 
> 
>
-- 
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Re: [gmx-users] total charge of the system

2008-07-10 Thread Daniel Adriano Silva M 
Serdar.

If the "real charge" of your system is not zero and you are using PME, then
PME code will take account for any non-zero charge on the system and
neutralize it with an uniform background charge (
http://wiki.gromacs.org/index.php/Errors).
If your system is composed by a protein, then try first to check the charge
for every residue (maybe you found some aminoacid with a not integral
charge).
Please note that several times if your charge is very close to an integer,
this warning is generated as consequence of the " summation of many floating
point numbers", check this link:
http://www.gromacs.org/pipermail/gmx-users/2008-May/034092.html

However, your error is on the  3rd digit (by a magnitude of .004), on my
experience gromacs "round errors" are very close to the integer (e.g. Sytem
Charge = .998 or 1.02), then I recommend you to take a look on your
system.

Daniel

2008/7/10 serdar durdagi <[EMAIL PROTECTED]>:

> Dear all,
>
>
>
> In one of my simulations, total charge of the system is a noninteger number
> (like +15.996). I neutralized it with 16 chlorine atoms. I am using periodic
> boundary conditions. If I use the charge as it is, is it means infinite
> negative total charge on the system?
>
>
>
> Actually, when I check the simulation output parameters, it seems every
> thing okay..I am just curious if it's some thing wrong..
>
>
>
> Serdar
>
> --
> Gesendet von Yahoo! 
> Mail.
>
> Dem pfiffigeren Posteingang.
>
> ___
> gmx-users mailing listgmx-users@gromacs.org
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>
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Re: [gmx-users] total charge of the system

2008-07-10 Thread Justin A. Lemkul 
Sometimes when grompp reports the total charge, it shows up as a non-integer and 
can sometimes be attributed to a round-off error.  Just to be sure, check your 
topology to make sure you have integer charges on all components of your system.


-Justin

serdar durdagi wrote:

Dear all,

 

In one of my simulations, total charge of the system is a noninteger 
number (like +15.996). I neutralized it with 16 chlorine atoms. I am 
using periodic boundary conditions. If I use the charge as it is, is it 
means infinite negative total charge on the system?


 

Actually, when I check the simulation output parameters, it seems every 
thing okay..I am just curious if it's some thing wrong..


 


Serdar



Gesendet von Yahoo! Mail 
. 


Dem pfiffigeren Posteingang.




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--


Justin A. Lemkul
Graduate Research Assistant
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin


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