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[Backward mapping] POPS result atomistic structure missing molecules
- Pham
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2 years 4 months ago #9274
by Pham
[Backward mapping] POPS result atomistic structure missing molecules was created by Pham
Hi there,
I'm having some problem reverse mapping POPS from martini coarse-grained to AMBER atomistic resolution.
At first, the Mapping I got from Tsjerk's Backward GITHUB does not match with the proposed martini lipid beads. Thus, I swapped tail A and tail B labels, as well as combining the original mapping beads C1B and C2B -> C1A to match with the double-bond and the amount of bead we had in CG (4 beads).
I checked and the mapping has 127 atoms, matched with the SLIPID/AMBER itp file.
When I run testing on backward mapping for 1 molecule of POPS, the backward.py passed without crashing. HOWEVER, the generated initial structure (projected.gro and 0-backmapped.gro) only has 102 molecules, instead of expecting 127 molecules. The ERROR from the initram.sh (at grompp of 1-EM) is:
Program grompp_mpi, VERSION 4.6.7
Source code file: /usr/local/gromacs-4.6.7/src/kernel/grompp.c, line: 598
Fatal error:
number of coordinates in coordinate file (0-backward.gro, 102)
does not match topology (backmapped.top, 127)
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors
[/color]
The files I used are in this Google Drive folder:
https://drive.google.com/drive/folders/1DEcKJxH3ljn5HTvtAku3p-NI3x5ZRxAA?usp=sharinghttps://drive.google.com/drive/folders/1DEcKJxH3ljn5HTvtAku3p-NI3x5ZRxAA?usp=sharing
And the command I executed is:
$ ./initram.sh -p topol-POPS-only.top -f POPS-only.pdb -o POPS-aa.gro -to amber99sb
This is the first time I experience this error, and I'm not familiar with python so I cannot debug the backward.py myself. Please help me with this problem. I appreciate your time reading this :).
I'm having some problem reverse mapping POPS from martini coarse-grained to AMBER atomistic resolution.
At first, the Mapping I got from Tsjerk's Backward GITHUB does not match with the proposed martini lipid beads. Thus, I swapped tail A and tail B labels, as well as combining the original mapping beads C1B and C2B -> C1A to match with the double-bond and the amount of bead we had in CG (4 beads).
I checked and the mapping has 127 atoms, matched with the SLIPID/AMBER itp file.
When I run testing on backward mapping for 1 molecule of POPS, the backward.py passed without crashing. HOWEVER, the generated initial structure (projected.gro and 0-backmapped.gro) only has 102 molecules, instead of expecting 127 molecules. The ERROR from the initram.sh (at grompp of 1-EM) is:
Program grompp_mpi, VERSION 4.6.7
Source code file: /usr/local/gromacs-4.6.7/src/kernel/grompp.c, line: 598
Fatal error:
number of coordinates in coordinate file (0-backward.gro, 102)
does not match topology (backmapped.top, 127)
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors
[/color]
The files I used are in this Google Drive folder:
https://drive.google.com/drive/folders/1DEcKJxH3ljn5HTvtAku3p-NI3x5ZRxAA?usp=sharinghttps://drive.google.com/drive/folders/1DEcKJxH3ljn5HTvtAku3p-NI3x5ZRxAA?usp=sharing
And the command I executed is:
$ ./initram.sh -p topol-POPS-only.top -f POPS-only.pdb -o POPS-aa.gro -to amber99sb
This is the first time I experience this error, and I'm not familiar with python so I cannot debug the backward.py myself. Please help me with this problem. I appreciate your time reading this :).
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