backward.py not able to unbreak molecules
- sdixit
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5 years 11 months ago #7644
by sdixit
backward.py not able to unbreak molecules was created by sdixit
Hi,
I've been trying to backward.py for CG -> AA conversion but I'm having problems with the initram.sh and backward.py. I've posted another forum on not matching the nomenclature on .pdb and .top/.itp. However, I'm also having the following error when I just try running backward.py.
(py27) [sugyan@bruotolo-serv notusingpdb2gmx]$ python backward.py -f cg_iappdimer_antiparallel.pdb -o backmapped.gro -p topol.top -to charmm36 -mapdir Mapping -po backmapped.top
Non-invertable box. Not able to unbreak molecules...
Traceback (most recent call last):
File "backward.py", line 660, in <module>
struc = Structure(options["-f"].value,strict=options["-strict"].value)
File "backward.py", line 374, in __init__
termini = [ is_terminal(i,j,A,B) for i,j in zip([False]+protein,protein+[False]) ]
File "backward.py", line 316, in is_terminal
return not a or not b or dist(a,b,box,invbox) > 0.7
File "backward.py", line 220, in dist
inv = m_inv(box)
File "backward.py", line 208, in m_inv
d = 1.0/det(A)
ZeroDivisionError: float division by zero
Is that because of not setting up a pbc? I used a pdb structure for martinize to create the CG .pdb file using the atomistic topology file that I created from pdb2gmx on the same pdb structure I used for martinize.
Now, when I have the option '-nopbc', it outputs the backmapped .gro file. But the structure is broken (not just visualization, I also tried calculating cross section with the given coordinates and get a terrible unexpected value out).
Help would be greatly appreciated!
I've been trying to backward.py for CG -> AA conversion but I'm having problems with the initram.sh and backward.py. I've posted another forum on not matching the nomenclature on .pdb and .top/.itp. However, I'm also having the following error when I just try running backward.py.
(py27) [sugyan@bruotolo-serv notusingpdb2gmx]$ python backward.py -f cg_iappdimer_antiparallel.pdb -o backmapped.gro -p topol.top -to charmm36 -mapdir Mapping -po backmapped.top
Non-invertable box. Not able to unbreak molecules...
Traceback (most recent call last):
File "backward.py", line 660, in <module>
struc = Structure(options["-f"].value,strict=options["-strict"].value)
File "backward.py", line 374, in __init__
termini = [ is_terminal(i,j,A,B) for i,j in zip([False]+protein,protein+[False]) ]
File "backward.py", line 316, in is_terminal
return not a or not b or dist(a,b,box,invbox) > 0.7
File "backward.py", line 220, in dist
inv = m_inv(box)
File "backward.py", line 208, in m_inv
d = 1.0/det(A)
ZeroDivisionError: float division by zero
Is that because of not setting up a pbc? I used a pdb structure for martinize to create the CG .pdb file using the atomistic topology file that I created from pdb2gmx on the same pdb structure I used for martinize.
Now, when I have the option '-nopbc', it outputs the backmapped .gro file. But the structure is broken (not just visualization, I also tried calculating cross section with the given coordinates and get a terrible unexpected value out).
Help would be greatly appreciated!
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- riccardo
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5 years 11 months ago #7645
by riccardo
Replied by riccardo on topic backward.py not able to unbreak molecules
When do you exactly mean by "when I have the option -nopbc"? At which stage did you use it? or by "Is that because of not setting up a pbc?"?
Does backmapping the "whole" CG structure (i.e., the CG structure which results from running the command: gmx trjconv -f not_whole.gro -o whole.gro -pbc whole) work?
Does backmapping the "whole" CG structure (i.e., the CG structure which results from running the command: gmx trjconv -f not_whole.gro -o whole.gro -pbc whole) work?
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- sdixit
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5 years 11 months ago #7647
by sdixit
Replied by sdixit on topic backward.py not able to unbreak molecules
It's not a trajectory file. But I used gmx editconf to add pbc to the structure and used backward.py, I still get the same error
Non-invertable box. Not able to unbreak molecules...
Backward.py has the option '-nopbc'. So I used that option when I was executing the python code.
Non-invertable box. Not able to unbreak molecules...
Backward.py has the option '-nopbc'. So I used that option when I was executing the python code.
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- z.sichaib
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5 years 8 months ago #7753
by z.sichaib
Replied by z.sichaib on topic backward.py not able to unbreak molecules
Dears,
I'm having the same problem:
I'm using the following command to backmap a CG protein to AA:
./initram-v5.sh -f protein_CG.gro -o protein_aa.gro -to amber -p topol.top
The program runs without any issues but when I visualize the AA structure, this later is weird. It looks broken, fragmented into 8 different pieces (?). I don't know if it's a PBC problem or something else. You can see a picture of how the final aa system looks like here: www.dropbox.com/s/smncxffmfz7ztd9/backmap.png?dl=0
@sdixit: I would like to know if you fixed your problem? If yes, can I have your feedback, please? How did you do to successfully backmap your system?
I would really appreciate any help/ advice from this community, please.
I'm having the same problem:
I'm using the following command to backmap a CG protein to AA:
./initram-v5.sh -f protein_CG.gro -o protein_aa.gro -to amber -p topol.top
The program runs without any issues but when I visualize the AA structure, this later is weird. It looks broken, fragmented into 8 different pieces (?). I don't know if it's a PBC problem or something else. You can see a picture of how the final aa system looks like here: www.dropbox.com/s/smncxffmfz7ztd9/backmap.png?dl=0
@sdixit: I would like to know if you fixed your problem? If yes, can I have your feedback, please? How did you do to successfully backmap your system?
I would really appreciate any help/ advice from this community, please.
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- riccardo
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5 years 6 months ago #7820
by riccardo
Replied by riccardo on topic backward.py not able to unbreak molecules
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