normal transformation of .xtc cg file to .xtc gro file

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3 months 1 week ago #7690 by cm
cm created the topic: transformation of .xtc cg file to .xtc gro file
hi,
i have already done the coarse grained.gro to all atom.gro.is it possible to convert a coarse grained.xtc file to all atom.xtc file.if possible...can anyone please help me how i can do this.
thanking you

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3 months 1 week ago #7691 by riccardo
riccardo replied the topic: transformation of .xtc cg file to .xtc gro file
I think that backward ( cgmartini.nl/index.php/tutorials-general...others-gmx5#Backward ) works also on xtc files (even though I never used it that way). Otherwise, just convert the xtc to gro (with gmx trjconv) beforehand.

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3 months 1 week ago #7692 by cm
cm replied the topic: transformation of .xtc cg file to .xtc gro file
thank you so much for your reply.
./initram.sh -f dynamic.xtc -o aa_charmm.gro -to charmm36 -p topol.top when i am using this command the error is
ValueError: invalid literal for int() with base 10: 'DF_8\xe5/\x89[\x85Z\xf5\xe1:R\xe3\xc13\xc6\xd2\xec"\xb9y\xe6\x1a\xac\xfbE\xac\xfb$Sx\x01Q{\xf0\xb1'
but i have converted the coarse graied to all atom .gro file.
i have done a coarse grained simulation for 10 microsecond.i have followed this
tutorial cgmartini.nl/index.php/tutorials-general-introduction/proteins .
basicaly for each micro second gap i have converted 10 coarse grained gro file to all atom gro file because in case of martini cg protein we can not calculate the secondary structure change.for this reason to calculate the change of secondary structure i just convert it in all atom gro file.but the problem is during the do_dssp ,i used this
do_dssp -s aa_charmm-300k-eq.gro -n ../index2.ndx -f ../pbc.xtc/md-5-6.xtc -sc scount-p2-5-6.xvg -o ss-p2-5-6.xpm -dt 10
where the .xtc is the file which i got from the coarse grained simulation.
is this .xtc will hamper the do_dssp analysis.
from the vmd, i am able to see the change of secondary structure but during do_dssp there is no change of secondary structure.
can you please tell me what i am doing wrong to calculate the each 1 microsecond gap secondary structure analysis of the .gro file.
thanking you

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3 months 1 week ago #7693 by riccardo
riccardo replied the topic: transformation of .xtc cg file to .xtc gro file
I am not sure about the do_dssp part. However, if the problem is really the xtc, you can convert the trajectory in a GRO file and try to feed it to the procedure, e.g.:

gmx trjconv -f traj.xtc -o traj.gro -s topol.tpr

where you just get the whole trajectory as a GRO file (the "traj.gro") or split it in frames with:

gmx trjconv -f traj.xtc -o frame.gro -s topol.tpr -sep

and just do your procedure (which works for a frame, as I understand) iteratively.

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