[gmx-users] total charge of the system
ahmet yıldırım
ahmedo047 at gmail.com
Tue Jan 25 12:27:08 CET 2011
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?
*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 <mark.abraham at anu.edu.au> yazdı:
>
>
> On 01/25/11, *ahmet yıldırım * <ahmedo047 at gmail.com> 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.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 .
>> 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
>> 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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>> Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>
>
>
> --
> 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
> www interface or send it to gmx-users-request at gromacs.org.
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>
--
Ahmet YILDIRIM
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