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error when using g_fg2cg
- Leliel
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10 years 8 months ago #1855
by Leliel
error when using g_fg2cg was created by Leliel
Hi,
i am using your 3.3.1-version g_fg2cg tool to do a reverse transformation.
when i type the command and press enter,there come lots of warning and a fatal error:
warning are all like this :
topol_DNA_chain_B.itp:388:38: warning: missing terminating ' character
topol_DNA_chain_B.itp:389:38: warning: missing terminating ' character
topol_DNA_chain_B.itp:390:38: warning: missing terminating ' character
topol_DNA_chain_B.itp:391:38: warning: missing terminating ' character
topol_DNA_chain_B.itp:392:38: warning: missing terminating ' character
and the fatal error is:
Invalid dihedral type 9
i do the fine grained MD in gromacs-4.6.2,and use the latest amber99sb-lin forcefield,and actually i copy these top directory in my 3.3.1's top to avoid a fatal error, but here comes another one? what is type 9 and in which files?
and should do all the simulation in 3.3.1?? cause i only have mdrun-coarse and g_fg2cg in version 3.3.1/
thanks in advance!
i am using your 3.3.1-version g_fg2cg tool to do a reverse transformation.
when i type the command and press enter,there come lots of warning and a fatal error:
warning are all like this :
topol_DNA_chain_B.itp:388:38: warning: missing terminating ' character
topol_DNA_chain_B.itp:389:38: warning: missing terminating ' character
topol_DNA_chain_B.itp:390:38: warning: missing terminating ' character
topol_DNA_chain_B.itp:391:38: warning: missing terminating ' character
topol_DNA_chain_B.itp:392:38: warning: missing terminating ' character
and the fatal error is:
Invalid dihedral type 9
i do the fine grained MD in gromacs-4.6.2,and use the latest amber99sb-lin forcefield,and actually i copy these top directory in my 3.3.1's top to avoid a fatal error, but here comes another one? what is type 9 and in which files?
and should do all the simulation in 3.3.1?? cause i only have mdrun-coarse and g_fg2cg in version 3.3.1/
thanks in advance!
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- djurre
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10 years 8 months ago - 10 years 8 months ago #1856
by djurre
Replied by djurre on topic error when using g_fg2cg
Going from fine grain to Coarse grain, there are better options then using the gromacs 3.3.1.
- If you have proteins only, you can transform you trajectory to a gro/pdb trajectory and use martinize.py
- Create an index file with one group for every bead and use g_traj/trjconv. For large or many molecules this can be a bit annoying.
- Use the new backward script (see downloads >> tools).
- Create an index file with one group for every bead and use g_traj/trjconv. For large or many molecules this can be a bit annoying.
- Use the new backward script (see downloads >> tools).
Last edit: 10 years 8 months ago by Clement.
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- Leliel
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10 years 8 months ago #1857
by Leliel
Replied by Leliel on topic error when using g_fg2cg
it's challenging that i am using martini FF to build a new DNA-model，so maybe the martinize.py and some other tools do little help to me.
so i will do all my simulation in 3.3.1/
thx a lot!!
so i will do all my simulation in 3.3.1/
thx a lot!!
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- Clement
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10 years 8 months ago - 10 years 8 months ago #1858
by Clement
Replied by Clement on topic error when using g_fg2cg
Mmmmh... Not to be insisting here, but for fine-grain-to-coarse-grain transformation there's no easier method than what Djurre advised you above. Creating an index file with one group for each bead is not that complicated to do; writing a script taking your mapping and returning the index file isn't a waste of time.
What exactly do you think you'll fix by doing everything with GROMACS 3.3.1? I'm quite sure you're not gonna fix anything, and come back to the solution described above...
What exactly do you think you'll fix by doing everything with GROMACS 3.3.1? I'm quite sure you're not gonna fix anything, and come back to the solution described above...
Last edit: 10 years 8 months ago by Clement.
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- Leliel
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10 years 8 months ago #1885
by Leliel
Replied by Leliel on topic error when using g_fg2cg
well，the point is that i am following a tutorial to create a DNA model,but the tool g_fg2cg seems not to recognize the input files.(as the first floor shows) i supposed that that maybe i use a advanced AT-FF (amber) that cant be recognized by gromacs-3.3.1/
then i wanna do a fine-grained MD in gromacs-3.3.1,but when i use pdb2mgx and choose the FF,there are always Fatal errors.
maybe this may be not good.
so how can i figure this out?
then i wanna do a fine-grained MD in gromacs-3.3.1,but when i use pdb2mgx and choose the FF,there are always Fatal errors.
maybe this may be not good.
so how can i figure this out?
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- djurre
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10 years 8 months ago #1887
by djurre
Replied by djurre on topic error when using g_fg2cg
You didn't give any new information in your last message, so let me also repeat what we said before: there are probably easier ways to do what you want to do than using the old gmx331.
That said, is there a message with the Fatal Errors? Are they still the ones from your first message? Than you should check your itp for errors. If I remember well the "missing dihedral 9" is often due to having the mapping section in you itp (and not out-commented) while you are not doing a mapping simulation.
If that doesn't solve the problem, paste your itp here so we can check it.
That said, is there a message with the Fatal Errors? Are they still the ones from your first message? Than you should check your itp for errors. If I remember well the "missing dihedral 9" is often due to having the mapping section in you itp (and not out-commented) while you are not doing a mapping simulation.
If that doesn't solve the problem, paste your itp here so we can check it.
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