subject:"\[gmx\-users\] grompp gives no molecules were defined in the system"

Re: [gmx-users] grompp gives "no molecules were defined in the system"

2010-01-28 Thread Justin A. Lemkul




Marysa van den Berg wrote:

Hi,
 
The number of atoms in the second line of my .gro file are correct, I 
checked that.
 
This is what my topology file says in the beginning:
 
[ moleculetype ]

; Name  nrexcl
Protein  3
 
No changes here after the solvation.
 
At the end after the [ atoms ] directive:
 
; Include Position restraint file

#ifdef POSRES
#include "posre.itp"
#endif
 
; Strong po

sition restraints for InflateGro
#ifdef STRONG_POSRES
#include "strong_posre.itp"
endif
 


Here's the problem.  To end the #ifdef statement, you need "#endif", not 
"endif."  Since you haven't closed the #ifdef, nothing is being found after this 
point in the topology (assuming you're not specifying "define = -DSTRONG_POSRES" 
in the .mdp file, which you only want at certain times).


-Justin


; Include DPPC chain topology
#include "dppc.itp"
 
; Include water topology

#include "spc.itp"
 
#ifdef POSRES_WATER

; Position restraint for each water oxygen
[ position_restraints ]
; i funct fcxfcy  fcz
  11   1000 1000 1000
#endif
 
; Include generic topology for ions

#include "ions.itp"
 
[ system ]

; Name
Protein
 
[ molecules ]

; Compound #mols
Protein1
DPPC  242
SOL   48333
 
The only thing in the topology that changed after the solvation, was 
adding the watermolecules in the [ molecules ] section (SOL 48333)

What could be the problem?
 
Thanks,
 
Marysa



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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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RE: [gmx-users] grompp gives "no molecules were defined in the system"

2010-01-28 Thread Marysa van den Berg


Hi,

 

The number of atoms in the second line of my .gro file are correct, I checked 
that.

 

This is what my topology file says in the beginning:

 

[ moleculetype ]

; Name  nrexcl

Protein  3

 

No changes here after the solvation.

 

At the end after the [ atoms ] directive:

 

; Include Position restraint file

#ifdef POSRES

#include "posre.itp"

#endif

 

; Strong po

sition restraints for InflateGro

#ifdef STRONG_POSRES

#include "strong_posre.itp"

endif

 

; Include DPPC chain topology

#include "dppc.itp"

 

; Include water topology

#include "spc.itp"

 

#ifdef POSRES_WATER

; Position restraint for each water oxygen

[ position_restraints ]

; i funct fcxfcy  fcz

  11   1000 1000 1000

#endif

 

; Include generic topology for ions

#include "ions.itp"

 

[ system ]

; Name

Protein

 

[ molecules ]

; Compound #mols

Protein1

DPPC  242

SOL   48333

 

The only thing in the topology that changed after the solvation, was adding the 
watermolecules in the [ molecules ] section (SOL 48333)

What could be the problem?

 

Thanks,

 

Marysa
  
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Re: [gmx-users] grompp gives "no molecules were defined in the system"

2010-01-28 Thread Justin A. Lemkul



Do you have the right number of atoms indicated on the second line of the .gro 
file?  What is in your [molecules] directive in your topology?


-Justin

Marysa van den Berg wrote:

Hi,
 
I have a problem with Gromacs. I want to do MD simulations with my 
proteïn in a DPPC-membrane.
Therefore I followed Justin Lemkul's tutorial on membrane proteïn 
simulation. I just used a bigger
membrane (256 lipids instead of 128). I managed to correctly embed the 
proteïn in the bilayer,
I solvated it with genbox and then I want to add ions. But when I use 
grompp to get a .tpr

file for genion, Gromacs fives the following error:
 
/Program grompp, VERSION 4.0.7

Source code file: ../../gromacs-4.0.7/src/kernel/grompp.c, line: 320/
/Fatal error:
No molecules were defined in the system
/
I did update my topology in the [ molecules ] section and checked it 
twice to see if it fits with
the .gro file. It is correct, so I don't know what the problem is. 
Before the solvation there was
no problem with grompp, so it must have something to do with the 
solvation? I hope someone

can help me.
 
Thanks,
 
Marysa van den Berg



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--


Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
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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Re: [gmx-users] grompp gives "no molecules were defined in the system"

2010-01-28 Thread Tsjerk Wassenaar

Hi Marysa,

The error is about the definition of mulecules, which suggests that
there are no [ moleculetype ] directives. Did you #include the proper
.itp file(s) with the necessary moleculetype definitions? If not,
you'll have to provide more information, probably posting the topology
file itself.

Cheers,

Tsjerk

On Thu, Jan 28, 2010 at 12:27 PM, Marysa van den Berg
 wrote:
> Hi,
>
> I have a problem with Gromacs. I want to do MD simulations with my proteïn
> in a DPPC-membrane.
> Therefore I followed Justin Lemkul's tutorial on membrane proteïn
> simulation. I just used a bigger
> membrane (256 lipids instead of 128). I managed to correctly embed the
> proteïn in the bilayer,
> I solvated it with genbox and then I want to add ions. But when I use grompp
> to get a .tpr
> file for genion, Gromacs fives the following error:
>
> Program grompp, VERSION 4.0.7
> Source code file: ../../gromacs-4.0.7/src/kernel/grompp.c, line: 320
> Fatal error:
> No molecules were defined in the system
>
> I did update my topology in the [ molecules ] section and checked it twice
> to see if it fits with
> the .gro file. It is correct, so I don't know what the problem is. Before
> the solvation there was
> no problem with grompp, so it must have something to do with the solvation?
> I hope someone
> can help me.
>
> Thanks,
>
> Marysa van den Berg
>
> 
> Minder SPAM in de verbeterde Windows Live Hotmail
> --
> gmx-users mailing list    gmx-us...@gromacs.org
> http://lists.gromacs.org/mailman/listinfo/gmx-users
> Please search the archive at http://www.gromacs.org/search before posting!
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> www interface or send it to gmx-users-requ...@gromacs.org.
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>



-- 
Tsjerk A. Wassenaar, Ph.D.

Computational Chemist
Medicinal Chemist
Neuropharmacologist
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[gmx-users] grompp gives "no molecules were defined in the system"

2010-01-28 Thread Marysa van den Berg


Hi,

 

I have a problem with Gromacs. I want to do MD simulations with my proteïn in a 
DPPC-membrane.

Therefore I followed Justin Lemkul's tutorial on membrane proteïn simulation. I 
just used a bigger

membrane (256 lipids instead of 128). I managed to correctly embed the proteïn 
in the bilayer,

I solvated it with genbox and then I want to add ions. But when I use grompp to 
get a .tpr

file for genion, Gromacs fives the following error:

 

Program grompp, VERSION 4.0.7
Source code file: ../../gromacs-4.0.7/src/kernel/grompp.c, line: 320

Fatal error:
No molecules were defined in the system


I did update my topology in the [ molecules ] section and checked it twice to 
see if it fits with

the .gro file. It is correct, so I don't know what the problem is. Before the 
solvation there was

no problem with grompp, so it must have something to do with the solvation? I 
hope someone

can help me.

 

Thanks,

 

Marysa van den Berg
  
_
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gmx-users mailing listgmx-users@gromacs.org
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Re: [gmx-users] grompp gives "no molecules were defined in the system"

RE: [gmx-users] grompp gives "no molecules were defined in the system"

Re: [gmx-users] grompp gives "no molecules were defined in the system"

Re: [gmx-users] grompp gives "no molecules were defined in the system"

[gmx-users] grompp gives "no molecules were defined in the system"

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