normal conversion of a POPC/DOPE bilayer plus water from CG to FG g_fg2cg

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12 years 11 months ago - 12 years 11 months ago #625 by liguori
Hi.
After having assembled my 85 POPC/43 DOPE membrane in 960 molecules of water, I'm trying to convert my CG coordinate file into a FG one. But I find always errors running g_fg2cg_d:

Tried to execute: 'cpp -I/Users/ph/local/gromacs-3.3.1/share/gromacs/top/ popc_dope_FG.top > gromppFmizE5'
The 'cpp' command is defined in the .mdp file
processing topology...
ERROR 1 : Incorrect number of atomtypes for dihedral (0 instead of 2 or 4) ERROR 2 [file "popc.itp", line 3]: Incorrect number of atomtypes for dihedral (1 instead of 2 or 4) Cleaning up temporary file gromppFmizE5 ------------------------------------------------------- Program g_fg2cg_d, VERSION 3.3.1 Source code file: ../kernel/topio.c, line: 477 Fatal error: Invalid order for directive atoms, file ""popc.itp"", line 5 ------------------------------------------------------- and this is one of the usual errors I find, the other is, when I use my topology file lipid.itp instead of one of those downloaded from martini tutorial, is: calling cpp... processing topology... Cleaning up temporary file gromppf40ZdS ------------------------------------------------------- Program g_fg2cg_d, VERSION 3.3.1 Source code file: ../kernel/toputil.c, line: 61 Fatal error: Atomtype 'C' not found! ------------------------------------------------------- I've already checked the numbers of W molecules and the way I have to write my bilayerFG.top file and I'm not able to make it work. thank you nicoletta[file "popc.itp", line 1]:
Incorrect number of atomtypes for dihedral (0 instead of 2 or 4)
ERROR 2 : Incorrect number of atomtypes for dihedral (1 instead of 2 or 4) Cleaning up temporary file gromppFmizE5 ------------------------------------------------------- Program g_fg2cg_d, VERSION 3.3.1 Source code file: ../kernel/topio.c, line: 477 Fatal error: Invalid order for directive atoms, file ""popc.itp"", line 5 ------------------------------------------------------- and this is one of the usual errors I find, the other is, when I use my topology file lipid.itp instead of one of those downloaded from martini tutorial, is: calling cpp... processing topology... Cleaning up temporary file gromppf40ZdS ------------------------------------------------------- Program g_fg2cg_d, VERSION 3.3.1 Source code file: ../kernel/toputil.c, line: 61 Fatal error: Atomtype 'C' not found! ------------------------------------------------------- I've already checked the numbers of W molecules and the way I have to write my bilayerFG.top file and I'm not able to make it work. thank you nicoletta[file "popc.itp", line 3]:
Incorrect number of atomtypes for dihedral (1 instead of 2 or 4)
Cleaning up temporary file gromppFmizE5
Program g_fg2cg_d, VERSION 3.3.1
Source code file: ../kernel/topio.c, line: 477

Fatal error:
Invalid order for directive atoms, file ""popc.itp"", line 5
and this is one of the usual errors I find,
the other is, when I use my topology file lipid.itp instead of one of those downloaded from martini tutorial,
is:


calling cpp...
processing topology...
Cleaning up temporary file gromppf40ZdS
Program g_fg2cg_d, VERSION 3.3.1
Source code file: ../kernel/toputil.c, line: 61

Fatal error:
Atomtype 'C' not found!
I've already checked the numbers of W molecules and the way I have to write my bilayerFG.top file and I'm not able to make it work.
thank you
nicoletta

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12 years 11 months ago #626 by xavier
Dear Liquori,

Did you check that the POPC/DOPE molecules have a mapping defined in the force field files?
It is a requirement. If it is not present you should include it yourself. You can use
other defined molecules as a guide.

XAvier

liguori wrote: Hi.
After having assembled my 85 POPC/43 DOPE membrane in 960 molecules of water, I'm trying to convert my CG coordinate file into a FG one. But I find always errors running g_fg2cg_d:

Tried to execute: 'cpp -I/Users/ph/local/gromacs-3.3.1/share/gromacs/top/ popc_dope_FG.top > gromppFmizE5'
The 'cpp' command is defined in the .mdp file
processing topology...
ERROR 1 : Incorrect number of atomtypes for dihedral (0 instead of 2 or 4) ERROR 2 [file "popc.itp", line 3]: Incorrect number of atomtypes for dihedral (1 instead of 2 or 4) Cleaning up temporary file gromppFmizE5 ------------------------------------------------------- Program g_fg2cg_d, VERSION 3.3.1 Source code file: ../kernel/topio.c, line: 477 Fatal error: Invalid order for directive atoms, file ""popc.itp"", line 5 ------------------------------------------------------- and this is one of the usual errors I find, the other is, when I use my topology file lipid.itp instead of one of those downloaded from martini tutorial, is: calling cpp... processing topology... Cleaning up temporary file gromppf40ZdS ------------------------------------------------------- Program g_fg2cg_d, VERSION 3.3.1 Source code file: ../kernel/toputil.c, line: 61 Fatal error: Atomtype 'C' not found! ------------------------------------------------------- I've already checked the numbers of W molecules and the way I have to write my bilayerFG.top file and I'm not able to make it work. thank you nicoletta[/quote][file "popc.itp", line 1]:
Incorrect number of atomtypes for dihedral (0 instead of 2 or 4)
ERROR 2 : Incorrect number of atomtypes for dihedral (1 instead of 2 or 4) Cleaning up temporary file gromppFmizE5 ------------------------------------------------------- Program g_fg2cg_d, VERSION 3.3.1 Source code file: ../kernel/topio.c, line: 477 Fatal error: Invalid order for directive atoms, file ""popc.itp"", line 5 ------------------------------------------------------- and this is one of the usual errors I find, the other is, when I use my topology file lipid.itp instead of one of those downloaded from martini tutorial, is: calling cpp... processing topology... Cleaning up temporary file gromppf40ZdS ------------------------------------------------------- Program g_fg2cg_d, VERSION 3.3.1 Source code file: ../kernel/toputil.c, line: 61 Fatal error: Atomtype 'C' not found! ------------------------------------------------------- I've already checked the numbers of W molecules and the way I have to write my bilayerFG.top file and I'm not able to make it work. thank you nicoletta[/quote][file "popc.itp", line 3]:
Incorrect number of atomtypes for dihedral (1 instead of 2 or 4)
Cleaning up temporary file gromppFmizE5


Program g_fg2cg_d, VERSION 3.3.1
Source code file: ../kernel/topio.c, line: 477

Fatal error:
Invalid order for directive atoms, file ""popc.itp"", line 5
and this is one of the usual errors I find,
the other is, when I use my topology file lipid.itp instead of one of those downloaded from martini tutorial,
is:


calling cpp...
processing topology...
Cleaning up temporary file gromppf40ZdS
Program g_fg2cg_d, VERSION 3.3.1
Source code file: ../kernel/toputil.c, line: 61

Fatal error:
Atomtype 'C' not found!
I've already checked the numbers of W molecules and the way I have to write my bilayerFG.top file and I'm not able to make it work.
thank you
nicoletta

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  • liguori
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12 years 11 months ago #628 by liguori
Hi Xavier,
thanks for your answer!!! I added a mapping to both POPC an DOPE but it's still not working!

Option Filename Type Description
-pfg popc_dope_FG_7april.top Input Topology file
-pcg popc_dope.top Input, Opt! Topology file
-c 85_popc_43_dope_water_secondassembly_new.gro Input Generic
trajectory: xtc trr trj gro g96 pdb
-o 85_popc_43_dope_water_secondassembly_new_FG.gro Output Generic
structure: gro g96 pdb xml

Option Type Value Description
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-nice int 0 Set the nicelevel
-n int 0 1: fg2cg transformation, 0: cg2fg transformation
-wat int 1 1: rewrites FG_CG water to true fg water;
-rad real 0.3 A radius for random atom insertion;

calling cpp...
popc_dope_FG_7april.top:1: error: #include expects "FILENAME" or <FILENAME>
cpp exit code: 256
Tried to execute: 'cpp -I/Users/ph/local/gromacs-3.3.1/share/gromacs/top/ popc_dope_FG_7april.top > gromppQCfc2A'
The 'cpp' command is defined in the .mdp file
processing topology...
Cleaning up temporary file gromppQCfc2A
Program g_fg2cg_d, VERSION 3.3.1
Source code file: ../kernel/topio.c, line: 477

Fatal error:
Invalid order for directive moleculetype, file ""popc_7april.itp"", line 1


But the real problem is that neither the tutorial exercise works .



Option Type Value Description
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-nice int 0 Set the nicelevel
-n int 0 1: fg2cg transformation, 0: cg2fg transformation
-wat int 0 1: rewrites FG_CG water to true fg water;
-rad real 0.3 A radius for random atom insertion;

calling cpp...
processing topology...
Generated 483 of the 1653 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.125
Generated 663 of the 1653 1-4 parameter combinations
Cleaning up temporary file gromppPMkGhr
Program g_fg2cg_d, VERSION 3.3.1
Source code file: ../kernel/topio.c, line: 303

Fatal error:
Invalid Atomnr j: 51, b2->nr: 50

And now I really don't know what to do.
Thank you again
Nicoletta

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12 years 11 months ago #630 by xavier

liguori wrote: Hi Xavier,
thanks for your answer!!! I added a mapping to both POPC an DOPE but it's still not working!

Option Filename Type Description


-pfg popc_dope_FG_7april.top Input Topology file
-pcg popc_dope.top Input, Opt! Topology file
-c 85_popc_43_dope_water_secondassembly_new.gro Input Generic
trajectory: xtc trr trj gro g96 pdb
-o 85_popc_43_dope_water_secondassembly_new_FG.gro Output Generic
structure: gro g96 pdb xml

Option Type Value Description
-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-nice int 0 Set the nicelevel
-n int 0 1: fg2cg transformation, 0: cg2fg transformation
-wat int 1 1: rewrites FG_CG water to true fg water;
-rad real 0.3 A radius for random atom insertion;

calling cpp...
popc_dope_FG_7april.top:1: error: #include expects "FILENAME" or <FILENAME>
cpp exit code: 256
Tried to execute: 'cpp -I/Users/ph/local/gromacs-3.3.1/share/gromacs/top/ popc_dope_FG_7april.top > gromppQCfc2A'
The 'cpp' command is defined in the .mdp file
processing topology...
Cleaning up temporary file gromppQCfc2A
Program g_fg2cg_d, VERSION 3.3.1
Source code file: ../kernel/topio.c, line: 477

Fatal error:
Invalid order for directive moleculetype, file ""popc_7april.itp"", line 1

Well this says that your topology file is wrong! you probably have missing or duplicate definition of directive ... see gromacs manual.


But the real problem is that neither the tutorial exercise works .



Option Type Value Description


-[no]h bool no Print help info and quit
-[no]X bool no Use dialog box GUI to edit command line options
-nice int 0 Set the nicelevel
-n int 0 1: fg2cg transformation, 0: cg2fg transformation
-wat int 0 1: rewrites FG_CG water to true fg water;
-rad real 0.3 A radius for random atom insertion;

calling cpp...
processing topology...
Generated 483 of the 1653 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.125
Generated 663 of the 1653 1-4 parameter combinations
Cleaning up temporary file gromppPMkGhr
Program g_fg2cg_d, VERSION 3.3.1
Source code file: ../kernel/topio.c, line: 303

Fatal error:
Invalid Atomnr j: 51, b2->nr: 50

I am not sure ... people have been through this tutorial and it seem to work fine for them. Try to understand where the problem is.


And now I really don't know what to do.
Thank you again
Nicoletta

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