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backward failing on multiple molecules
- ram74656
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Topic Author
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6 years 6 months ago #7394
by ram74656
backward failing on multiple molecules was created by ram74656
Hi,
I'm trying to get the backmapping functionality of initram and backward.py working, and it works just fine if I stick one of my coarse-grained monomers in solution and backmap (I've had to define new mapping files for some of my residues, and this went perfectly OK), but as soon as I try to do it with a system that contains multiple peptide monomers instead of just one, backward fails with:
Traceback (most recent call last):
File "/home/rachael/coarsegraining/finegraining/DFAG/size6/backmap/backward.py", line 659, in <module>
struc = Structure(options["-f"].value,strict=options["-strict"].value)
File "/home/rachael/coarsegraining/finegraining/DFAG/size6/backmap/backward.py", line 419, in __init__
d12.append(d12[-1])
IndexError: list index out of range
I'm confused as to why this is happening and would appreciate any guidance--I've tried two different .top files, in thinking that that might be the root of the problem, one with
[ molecules ]
; Compound #mols
Protein 6
and one with
[ molecules ]
; Compound #mols
Protein1 1
Protein2 1
Protein3 1
Protein4 1
Protein5 1
Protein6 1
where all 6 proteins are the same topology, just recopied, but both fail with the same error.
Thanks very much!
I'm trying to get the backmapping functionality of initram and backward.py working, and it works just fine if I stick one of my coarse-grained monomers in solution and backmap (I've had to define new mapping files for some of my residues, and this went perfectly OK), but as soon as I try to do it with a system that contains multiple peptide monomers instead of just one, backward fails with:
Traceback (most recent call last):
File "/home/rachael/coarsegraining/finegraining/DFAG/size6/backmap/backward.py", line 659, in <module>
struc = Structure(options["-f"].value,strict=options["-strict"].value)
File "/home/rachael/coarsegraining/finegraining/DFAG/size6/backmap/backward.py", line 419, in __init__
d12.append(d12[-1])
IndexError: list index out of range
I'm confused as to why this is happening and would appreciate any guidance--I've tried two different .top files, in thinking that that might be the root of the problem, one with
[ molecules ]
; Compound #mols
Protein 6
and one with
[ molecules ]
; Compound #mols
Protein1 1
Protein2 1
Protein3 1
Protein4 1
Protein5 1
Protein6 1
where all 6 proteins are the same topology, just recopied, but both fail with the same error.
Thanks very much!
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- tsjerk
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6 years 6 months ago #7395
by tsjerk
Replied by tsjerk on topic backward failing on multiple molecules
Hi :)
That's really odd. Can you send me the CG structure and the AA topology stuff at tsjerkw _at_ gmail _dot_ com?
Cheers,
Tsjerk
That's really odd. Can you send me the CG structure and the AA topology stuff at tsjerkw _at_ gmail _dot_ com?
Cheers,
Tsjerk
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- ram74656
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6 years 6 months ago #7396
by ram74656
Replied by ram74656 on topic backward failing on multiple molecules
I'll do that, thank you very much.
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