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need help in running CG simulation
- alliki
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9 years 10 months ago #3888
by alliki
need help in running CG simulation was created by alliki
Dear users,
I want to run the CG simulation, I am fallowing the martini tutorial. The
./martinize.py worked well for me howerver I am a bit confussed regarding the next step. It is written that I should "Do a short (+/-10 steps!) minimization in vacuum. (Before you can generate the run-input files with grompp, you have to generate a box, for example using editconf)". I am not sure what should I do after running the ./martinize.py script. I tried to run the grompp with the new pdb file obtained after running script and I got: fatal error: Topology include file "martini.itp" not found". Then I tried to run pdb2gmx command using the file obatined from script, however I got also a fatal error: Incomplete ring in HIS24.
I am new to GROMACS and CG simulation. Thank you for any help and suggestions.
Best regards
Urszula
I want to run the CG simulation, I am fallowing the martini tutorial. The
./martinize.py worked well for me howerver I am a bit confussed regarding the next step. It is written that I should "Do a short (+/-10 steps!) minimization in vacuum. (Before you can generate the run-input files with grompp, you have to generate a box, for example using editconf)". I am not sure what should I do after running the ./martinize.py script. I tried to run the grompp with the new pdb file obtained after running script and I got: fatal error: Topology include file "martini.itp" not found". Then I tried to run pdb2gmx command using the file obatined from script, however I got also a fatal error: Incomplete ring in HIS24.
I am new to GROMACS and CG simulation. Thank you for any help and suggestions.
Best regards
Urszula
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- Clement
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9 years 9 months ago #3940
by Clement
Replied by Clement on topic need help in running CG simulation
Hi Urszula!
If you're new at GROMACS and Martini, I'd advise to follow the lipid tutorial first... Easiest way to learn all that in one go. :-)
Good luck!
If you're new at GROMACS and Martini, I'd advise to follow the lipid tutorial first... Easiest way to learn all that in one go. :-)
Good luck!
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