- Posts: 34
converting from cg to aa
i have followed this tutorial for martini cg simulation
now after the production run i want to convert the coarse grained file to all atom file.
now i am using this command
./initram-v5.sh -f dynamic.gro -o aa_charmm.gro -to charmm36 -p system.top
but afer this i am getting this error
backward.py ... /home/intel/cys-cg-300/backward.py
gmx ... Missing dependency: gmx
can anyone please help me how i will do this.
Just click on the link that says "The scripts and mapping definitions for gromacs versions 4 and 5-bead oleoyl lipid chains are combined into a single zip file, which can be downloaded here."
No such moleculetype SOL
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors
can you please tell me how i will do this.
Regarding how to make an atomsitic top file, you pick the atomistic force field of your preference and then make sure you have a topology for each molecule included in your backmapped configuration. See also this:
"A complete fine-grained force field corresponding to all the CG molecules in CG_posre.gro. Here we use CHARMM36, see all .itp files provided and topol.top, which contains the molecules in the same order they are present in CG_posre.gro and with the same names. Note, water and ions can be skipped in the .top files as they are automatically detected by backward.py."
in the tutorial http://cgmartini.nl/index.php/tutorials-general-introduction/others .
So, actually, you can skip the water (and ions) altogether in the top file.
after using this command
./initram.sh -f dynamic.gro -o aa_charmm.gro -to charmm36 -p topol.top
i have gotten three files backmapped.ndx,backmapped.top,aa_charmm.gro.
and now i am able to see the structure.