[gmx-users] total charge of the system
ahmet yıldırım
ahmedo047 at gmail.com
Tue Jan 25 11:44:29 CET 2011
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.Peter at 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 * <ahmedo047 at gmail.com> 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
> 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 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
> SOL 10
> SOL 127
> SOL 157
> SOL 4177*1*
> CL- *8*
>
>
> 25 Ocak 2011 10:49 tarihinde Mark Abraham <mark.abraham at anu.edu.au> yazdı:
>
>>
>>
>> On 01/25/11, *ahmet yıldırım * <ahmedo047 at gmail.com> wrote:
>>
>> Hi,
>>
>> In my simulation, total charge of the system is a noninteger number
>> (System has non-zero total charge: 8.000004e+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 at 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!
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>>
>
>
>
> --
> Ahmet YILDIRIM
>
>
> --
> gmx-users mailing list gmx-users at 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
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--
Ahmet YILDIRIM
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