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conversion from cg to all altom cotaining a system popc popg and protein
- cm
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4 years 7 months ago #8241
by cm
conversion from cg to all altom cotaining a system popc popg and protein was created by cm
hi,
my system consist of two different lipid, popc and popg, protein, ion, water . When i am trying to convert from cg to all atom system by using this command
./initram.sh -f *.gro -o aa_charmm.gro -to charmm36 -p topol.top
the coming fatal error is:
Atomtype Q0 not found
i have found that the first atom id of popc is Q0.
can anyone please guide me to solve this error.
thanking you
my system consist of two different lipid, popc and popg, protein, ion, water . When i am trying to convert from cg to all atom system by using this command
./initram.sh -f *.gro -o aa_charmm.gro -to charmm36 -p topol.top
the coming fatal error is:
Atomtype Q0 not found
i have found that the first atom id of popc is Q0.
can anyone please guide me to solve this error.
thanking you
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- riccardo
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4 years 7 months ago #8242
by riccardo
Replied by riccardo on topic conversion from cg to all altom cotaining a system popc popg and protein
The topolo.top should contain the atomistic topology. If my guess is right, now topol.top contains the CG one?
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4 years 7 months ago #8243
by cm
Replied by cm on topic conversion from cg to all altom cotaining a system popc popg and protein
thank you so much for your reply.
no the topol top contain the atomistic topology.
no the topol top contain the atomistic topology.
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4 years 7 months ago #8244
by riccardo
Replied by riccardo on topic conversion from cg to all altom cotaining a system popc popg and protein
First, just to be sure: are you using the latest backward version which can be found at
github.com/Tsjerk/Backward
?
Also, Q0 is a particle type in Martini, so what I don't understand is how do you get a "atom type not found" error if you are just reading in the coordinates of the CG.gro, that is, the CG topology - and hence CG atom types - shouldn't matter.
But maybe an atom type is called "Q0" also in charmm?
Also, Q0 is a particle type in Martini, so what I don't understand is how do you get a "atom type not found" error if you are just reading in the coordinates of the CG.gro, that is, the CG topology - and hence CG atom types - shouldn't matter.
But maybe an atom type is called "Q0" also in charmm?
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- cm
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4 years 7 months ago - 4 years 7 months ago #8246
by cm
Replied by cm on topic conversion from cg to all altom cotaining a system popc popg and protein
yes, you are right. I have included the atomistic itp file of protein in the top file but included martini itp of popc and popg lipid. Can you please guide me how i will get the atomistic itp file of popc and popg.
thanking you
thanking you
Last edit: 4 years 7 months ago by cm.
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4 years 7 months ago - 4 years 7 months ago #8248
by cm
Replied by cm on topic conversion from cg to all altom cotaining a system popc popg and protein
during backmapping i am getting this error
Please can you tell me what wrong i am doing.
Checking dependencies:
backward.py ... /home/intel/mem-prot/backward.py
grompp ... /usr/bin/grompp
mdrun ... /usr/bin/mdrun
Residues defined for transformation from martini to charmm36:
Problem determining mapping coordinates for atom N of residue POPG.
atomlist: 'C23', 'H3R', 'H3S', 'C24', 'H4R', 'H4S', 'C25', 'H5R', 'H5S', 'C26', 'H6R', 'H6S', 'C27', 'H7R', 'H7S', 'C28', 'H8R', 'H8S', 'C29', 'H91', 'C210', 'H101', 'C211', 'H11R', 'H11S', 'C212', 'H12R', 'H12S', 'C213', 'H13R', 'H13S', 'C214', 'H14R', 'H14S', 'C215', 'H15R', 'H15S', 'C216', 'H16R', 'H16S', 'C217', 'H17R', 'H17S', 'C218', 'H18R', 'H18S', 'H18T', 'C33', 'H3X', 'H3Y', 'C34', 'H4X', 'H4Y', 'C35', 'H5X', 'H5Y', 'C36', 'H6X', 'H6Y', 'C37', 'H7X', 'H7Y', 'C38', 'H8X', 'H8Y', 'C39', 'H9X', 'H9Y', 'C310', 'H10X', 'H10Y', 'C311', 'H11X', 'H11Y', 'C312', 'H12X', 'H12Y', 'C313', 'H13X', 'H13Y', 'C314', 'H14X', 'H14Y', 'C315', 'H15X', 'H15Y', 'C316', 'H16X', 'H16Y', 'H16Z']
want: N
have:
Bailing out..
thanking you
Please can you tell me what wrong i am doing.
Checking dependencies:
backward.py ... /home/intel/mem-prot/backward.py
grompp ... /usr/bin/grompp
mdrun ... /usr/bin/mdrun
Residues defined for transformation from martini to charmm36:
Problem determining mapping coordinates for atom N of residue POPG.
atomlist: 'C23', 'H3R', 'H3S', 'C24', 'H4R', 'H4S', 'C25', 'H5R', 'H5S', 'C26', 'H6R', 'H6S', 'C27', 'H7R', 'H7S', 'C28', 'H8R', 'H8S', 'C29', 'H91', 'C210', 'H101', 'C211', 'H11R', 'H11S', 'C212', 'H12R', 'H12S', 'C213', 'H13R', 'H13S', 'C214', 'H14R', 'H14S', 'C215', 'H15R', 'H15S', 'C216', 'H16R', 'H16S', 'C217', 'H17R', 'H17S', 'C218', 'H18R', 'H18S', 'H18T', 'C33', 'H3X', 'H3Y', 'C34', 'H4X', 'H4Y', 'C35', 'H5X', 'H5Y', 'C36', 'H6X', 'H6Y', 'C37', 'H7X', 'H7Y', 'C38', 'H8X', 'H8Y', 'C39', 'H9X', 'H9Y', 'C310', 'H10X', 'H10Y', 'C311', 'H11X', 'H11Y', 'C312', 'H12X', 'H12Y', 'C313', 'H13X', 'H13Y', 'C314', 'H14X', 'H14Y', 'C315', 'H15X', 'H15Y', 'C316', 'H16X', 'H16Y', 'H16Z']
want: N
have:
Bailing out..
thanking you
Last edit: 4 years 7 months ago by cm. Reason: all the lines are not uploaging
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4 years 7 months ago - 4 years 7 months ago #8250
by cm
Replied by cm on topic conversion from cg to all altom cotaining a system popc popg and protein
after downloading the new backward.py from git hub ...the new error arise
problem determinig mapping coordinate for atom C27 of residue POPC.
want C27
should be mapping from
[D2A]
Bailling out.
I can not understand this why this error is coming.
Please help me in this regards.
thanking you
problem determinig mapping coordinate for atom C27 of residue POPC.
want C27
should be mapping from
[D2A]
Bailling out.
I can not understand this why this error is coming.
Please help me in this regards.
thanking you
Last edit: 4 years 7 months ago by cm.
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