normal converting from cg to aa

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3 months 3 weeks ago #7679 by cm
cm created the topic: converting from cg to aa
hi,
i have followed this tutorial for martini cg simulation
cgmartini.nl/index.php/tutorials-general-introduction/proteins
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
Checking dependencies:
backward.py ... /home/intel/cys-cg-300/backward.py
gmx ... Missing dependency: gmx
can anyone please help me how i will do this.
thanking you

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3 months 3 weeks ago #7680 by riccardo
riccardo replied the topic: converting from cg to aa
This error message means that initram.sh is not able to find a GROMACS version (5.x or later) on your machine. Are you sure you have GROMACS available/sourced properly where you are running the backmapping command?

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3 months 3 weeks ago #7681 by cm
cm replied the topic: converting from cg to aa
thank so much for your reply.
yes the gromacs is already installed but the version is 4.5.5.

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3 months 3 weeks ago #7682 by riccardo
riccardo replied the topic: converting from cg to aa
Then you should use the initram/backward version compatible with GMX < 5. You can find it here:

cgmartini.nl/index.php/tools2/resolution-transformation

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."

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3 months 3 weeks ago #7683 by cm
cm replied the topic: converting from cg to aa
thank you so much.

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3 months 3 weeks ago #7684 by cm
cm replied the topic: converting from cg to aa
afetr this command i am getting this error
Fatal error:
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.

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3 months 3 weeks ago #7685 by riccardo
riccardo replied the topic: converting from cg to aa
Looks like there's no water (SOL=water) topology in your TOP file (the system.top). Is that so?

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3 months 3 weeks ago #7686 by cm
cm replied the topic: converting from cg to aa
yes the sol molecules are present in the topology file.here i am using coarse grained top file,should i use atomistic top file and if so then how i will make the atomistic top file.

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3 months 3 weeks ago #7687 by riccardo
riccardo replied the topic: converting from cg to aa
Yes, you must use a target atomistic topology. It is the atomistic topology which will be used by initram.sh to relax the backmapped coordinates to the local atomistic minimum after the projection made by backward (see also explanation in backward Tutorial and TA Wassenaar et al. J. Chem. Theory Comput., 2014, 10 (2), pp 676–690]

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.

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3 months 3 weeks ago - 3 months 3 weeks ago #7688 by cm
cm replied the topic: converting from cg to aa
thank you.
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.
Last Edit: 3 months 3 weeks ago by cm.

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