Re: [gmx-users] how to simulate a protein and a ATP molecule simultaneity?

[TJ Piggot]

Hi,

If you are using any of the united atom GROMOS96 forcefields then there is 
already an rtp entry for ATP. Check out the .rtp files in the top folder. 
All you need to do is to have the ATP atoms in the pdb file the same as the 
atom names in the .rtp file for pdb2gmx to do all the work for you. If you 
are not using a united atom forcefield then you will have to get your 
parameters for ATP from somewhere else (or calculate them yourself - not 
easy).


Hope this helps

Tom

--On Thursday, August 09, 2007 10:03:30 +0200 Maik Goette 
<[EMAIL PROTECTED]> wrote:



Be aware, that you can't use the ouput with every forcefield...
Attaching the gro-file to your protein gro at the proper position (right
after the protein) and building the correct topology should do the job.


Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
 mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


mjduan wrote:

Yes, I found a server (ProDrg) can get the .gro and .top files of ATP
molecule.


---
Whereas one should also mention, that ATP isn't included in every
forcefield, GROMACS supports...
So probably, parameterization has to be done also.

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Mark Abraham wrote:

mjduan at smail.hust.edu.cn wrote:

Dear GROMACS users:
I want to simulate a complex composed by a protein and an ATP
molecule,  and when I use the pdb2gmx to build the topology file and
transfer  the*pdb* file to *gro* file, it said "/Fatal error: Atom PG
in residue  ATP 1 not found in rtp entry with 36 atoms while sorting
atoms/", So how  can I build the *top* file and *gro* file for ATP
molecular and simulate  the protein molcular and ATP molecule
simultaneity?

By reading chapter 5 of the manual thoroughly, understanding how the rtp
files work for your force field and modifying your .pdb file and/or
force field files to work suitably.

Mark
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--
TJ Piggot
[EMAIL PROTECTED]
University of Bristol, UK.

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Re: [gmx-users] how to simulate a protein and a ATP molecule simultaneity?

[Maik Goette]

Be aware, that you can't use the ouput with every forcefield...
Attaching the gro-file to your protein gro at the proper position (right 
after the protein) and building the correct topology should do the job.



Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


mjduan wrote:

Yes, I found a server (ProDrg) can get the .gro and .top files of ATP
molecule.


---
Whereas one should also mention, that ATP isn't included in every
forcefield, GROMACS supports...
So probably, parameterization has to be done also.

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Mark Abraham wrote:

mjduan at smail.hust.edu.cn wrote:

Dear GROMACS users:
I want to simulate a complex composed by a protein and an ATP molecule, 
and when I use the pdb2gmx to build the topology file and transfer 
the*pdb* file to *gro* file, it said "/Fatal error: Atom PG in residue 
ATP 1 not found in rtp entry with 36 atoms while sorting atoms/", So how 
can I build the *top* file and *gro* file for ATP molecular and simulate 
the protein molcular and ATP molecule simultaneity?

By reading chapter 5 of the manual thoroughly, understanding how the rtp
files work for your force field and modifying your .pdb file and/or
force field files to work suitably.

Mark
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[gmx-users] how to simulate a protein and a ATP molecule simultaneity?

[mjduan]

Yes, I found a server (ProDrg) can get the .gro and .top files of ATP
molecule.


---
Whereas one should also mention, that ATP isn't included in every
forcefield, GROMACS supports...
So probably, parameterization has to be done also.

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Mark Abraham wrote:
> mjduan at smail.hust.edu.cn wrote:
>> Dear GROMACS users:
>> I want to simulate a complex composed by a protein and an ATP molecule, 
>> and when I use the pdb2gmx to build the topology file and transfer 
>> the*pdb* file to *gro* file, it said "/Fatal error: Atom PG in residue 
>> ATP 1 not found in rtp entry with 36 atoms while sorting atoms/", So how 
>> can I build the *top* file and *gro* file for ATP molecular and simulate 
>> the protein molcular and ATP molecule simultaneity?
> 
> By reading chapter 5 of the manual thoroughly, understanding how the rtp
> files work for your force field and modifying your .pdb file and/or
> force field files to work suitably.
> 
> Mark
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> 

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Re: [gmx-users] how to simulate a protein and a ATP molecule simultaneity?

[Maik Goette]

As Mark suggested. If you have the parameters for your ATP, build an
RTP-entry and afterwards, give the protein together with ATP into pdb2gmx...

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


[EMAIL PROTECTED] wrote:
> Thank u very much for your suggestion, and now I had get the .gro file 
> and .top file of ATP molecule, but how to I add the ATP molecule into 
> the .gro and .top files of the protein? (If I paste the ATP's datas to 
> the end of protein's file directly, and do genbox, then the result (.gro 
> /.top file) only contain the atoms of the protein and water.)
> And is there any difference between the .mdp file to do grompp for this 
> complex and for the system only contain protein and water?
> 
> 
> 
> 
> mjduan at smail.hust.edu.cn 
>  wrote:
>>/ Dear GROMACS users:
> />/ I want to simulate a complex composed by a protein and an ATP molecule, 
> />/ and when I use the pdb2gmx to build the topology file and transfer 
> />/ the*pdb* file to *gro* file,
>   it said "/Fatal error: Atom PG in residue 
> />/ ATP 1 not found in rtp entry with 36 atoms while sorting atoms/", So how 
> />/ can I build the *top* file and *gro* file for ATP molecular and simulate 
> />/ the protein molcular and ATP molecule simultaneity?
> /
> By reading chapter 5 of the manual thoroughly, understanding how the rtp
> files work for your force field and modifying your .pdb file and/or
> force field files to work suitably.
> 
> Mark
> 
> 
> 
> 
> 
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[gmx-users] how to simulate a protein and a ATP molecule simultaneity?

[mjduan]

Thank u very much for your suggestion, and now I had get the .gro file and .top file of ATP molecule, but how to I add the ATP molecule into the .gro and .top files of the protein? (If I paste the ATP's datas to the end of protein's file directly, and do genbox, then the result (.gro /.top file) only contain the atoms of the protein and water.) And is there any difference between the .mdp file to do grompp for this complex and for the system only contain protein and water?mjduan at smail.hust.edu.cn wrote:> Dear GROMACS users:> I want to simulate a complex composed by a protein and an ATP molecule, > and when I use the pdb2gmx to build the topology file and transfer > the*pdb* file to *gro* file,
  it said "/Fatal error: Atom PG in residue > ATP 1 not found in rtp entry with 36 atoms while sorting atoms/", So how > can I build the *top* file and *gro* file for ATP molecular and simulate > the protein molcular and ATP molecule simultaneity?By reading chapter 5 of the manual thoroughly, understanding how the rtpfiles work for your force field and modifying your .pdb file and/orforce field files to work suitably.Mark 

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Re: [gmx-users] how to simulate a protein and a ATP molecule simultaneity?

[Maik Goette]

Whereas one should also mention, that ATP isn't included in every
forcefield, GROMACS supports...
So probably, parameterization has to be done also.

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Mark Abraham wrote:
> [EMAIL PROTECTED] wrote:
>> Dear GROMACS users:
>> I want to simulate a complex composed by a protein and an ATP molecule, 
>> and when I use the pdb2gmx to build the topology file and transfer 
>> the*pdb* file to *gro* file, it said "/Fatal error: Atom PG in residue 
>> ATP 1 not found in rtp entry with 36 atoms while sorting atoms/", So how 
>> can I build the *top* file and *gro* file for ATP molecular and simulate 
>> the protein molcular and ATP molecule simultaneity?
> 
> By reading chapter 5 of the manual thoroughly, understanding how the rtp
> files work for your force field and modifying your .pdb file and/or
> force field files to work suitably.
> 
> Mark
> ___
> gmx-users mailing listgmx-users@gromacs.org
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> www interface or send it to [EMAIL PROTECTED]
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> 
> .
> 
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Re: [gmx-users] how to simulate a protein and a ATP molecule simultaneity?

[Mark Abraham]

[EMAIL PROTECTED] wrote:
> Dear GROMACS users:
> I want to simulate a complex composed by a protein and an ATP molecule, 
> and when I use the pdb2gmx to build the topology file and transfer 
> the*pdb* file to *gro* file, it said "/Fatal error: Atom PG in residue 
> ATP 1 not found in rtp entry with 36 atoms while sorting atoms/", So how 
> can I build the *top* file and *gro* file for ATP molecular and simulate 
> the protein molcular and ATP molecule simultaneity?

By reading chapter 5 of the manual thoroughly, understanding how the rtp
files work for your force field and modifying your .pdb file and/or
force field files to work suitably.

Mark
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[gmx-users] how to simulate a protein and a ATP molecule simultaneity?

[mjduan]

Dear GROMACS users:I want to simulate a complex composed by a protein and an ATP molecule, and when I use the pdb2gmx to build the topology file and transfer thepdb file to gro file, it said "Fatal error: Atom PG in residue ATP 1 not found in rtp entry with 36 atoms while sorting atoms", So how can I build the top file and gro file for ATP molecular and simulate the protein molcular and ATP molecule simultaneity?Best wishes!Mo-Jie Duan 

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