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problem with backward to construct CHARMM model
- Stéfane
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7 years 5 months ago #6007
by Stéfane
problem with backward to construct CHARMM model was created by Stéfane
Dear all,
I am interested to transform a CG surfactant system that contains AOT* into AA one (with the charmm27/36 rules). For that I have built my own map file and used it backward.py with the following command line (for testing)
./initram.sh -f 1_AOT_CG.gro -kick 0.5 -o 1.5us_AOT_RM_CG_AA.gro -p System_AA.top -from martini -to charmm36 -nopr -nb 1000 -em 1000 -keep
The 1_AOT_CG.gro file contains 1 AOT CG molecule. The backward.py script works at the beginning without any errors but the 0-backward.gro is empty so the script stops
I have a probably an error in my *.map file (witch is quite simple, for the moment) but I do not know where
Could you help me? You could download the necessary files by clicking on the following link:
drive.google.com/file/d/0B3sW6cS-tVa2TXZ...dG8/view?usp=sharing
* pubs.rsc.org/en/content/articlehtml/2014/sm/c4sm01763c
Thanks
Stéphane
I am interested to transform a CG surfactant system that contains AOT* into AA one (with the charmm27/36 rules). For that I have built my own map file and used it backward.py with the following command line (for testing)
./initram.sh -f 1_AOT_CG.gro -kick 0.5 -o 1.5us_AOT_RM_CG_AA.gro -p System_AA.top -from martini -to charmm36 -nopr -nb 1000 -em 1000 -keep
The 1_AOT_CG.gro file contains 1 AOT CG molecule. The backward.py script works at the beginning without any errors but the 0-backward.gro is empty so the script stops
I have a probably an error in my *.map file (witch is quite simple, for the moment) but I do not know where
Could you help me? You could download the necessary files by clicking on the following link:
drive.google.com/file/d/0B3sW6cS-tVa2TXZ...dG8/view?usp=sharing
* pubs.rsc.org/en/content/articlehtml/2014/sm/c4sm01763c
Thanks
Stéphane
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- riccardo
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7 years 2 months ago #6850
by riccardo
Replied by riccardo on topic problem with backward to construct CHARMM model
Hi Stéfane,
I see this question only now, hopefully my answer will still be useful.
I checked your aot.charm36.map file: you're missing a first column with the AA atom numbers in the [ atom ] sections. Please compare to the files in Mapping/gromos/.. (e.g., Mapping/gromos/dopc.gromos.map).
I see this question only now, hopefully my answer will still be useful.
I checked your aot.charm36.map file: you're missing a first column with the AA atom numbers in the [ atom ] sections. Please compare to the files in Mapping/gromos/.. (e.g., Mapping/gromos/dopc.gromos.map).
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