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Problems in converting coarse grained to all atom
- Diniz
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4 years 6 months ago #8269
by Diniz
Problems in converting coarse grained to all atom was created by Diniz
Hello!
My system is composed of a protein dimer (each domain with 131 residues) and 128 dppc molecules with water as solvent. A build the system with the dppc molecules placed randomly in the box and performed a 30 ns simulation with martini force field. Now I'm having problems in backmapping the system to all atom. I built the atomistic target topology using a extended version of the gromos54a7 force field that includes parameters for lipids. When I execute initram-v5.sh something weird happens. The 0-backward.gro generated in the first step misses all of the dppc molecules while the backmapped.top has, as expected, the 128 dppc molecules. The problem then arises when the scripts tries to execute the grompp for performing energy minimization, once topology and coordinate files doesn't have the same amount of atoms.
If anyone knows what I'm doing wrong I would appreciate the advice.
Here is the output of the failed initram-v5.sh execution:
initram.sh version 0.1:
(c)2013 Tsjerk A. Wassenaar, PhD
University of Calgary
2500 University Drive NW
Calgary, Alberta
Canada, T2N 1N4
Now executing...
./initram-v5.sh -f dynamics2.gro -p topol.top -po backmapped.top -o backmapped.gro -from martini -to gromos54a7
Checking dependencies:
backward.py ... /home/eduardo/bilayer/cg-to-aa/backward.py
gmx ... /usr/local/gromacs/bin/gmx
/home/eduardo/bilayer/cg-to-aa/backward.py -f dynamics2.gro -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p topol.top -po backmapped.top -n backmapped.ndx -from martini -to gromos54a7
Error reading charmm27 to martini mapping for POPG (file: /home/eduardo/bilayer/cg-to-aa/Mapping/popc.charmm36.map).
Error reading charmm36 to martini mapping for POPG (file: /home/eduardo/bilayer/cg-to-aa/Mapping/popc.charmm36.map).
Error reading slipids to martini mapping for POPG (file: /home/eduardo/bilayer/cg-to-aa/Mapping/popc.charmm36.map).
Error reading amber to martini mapping for POPG (file: /home/eduardo/bilayer/cg-to-aa/Mapping/popc.charmm36.map).
Error reading charmm27 to martini mapping for TOCL2 (file: /home/eduardo/bilayer/cg-to-aa/Mapping/asn.amber.map).
Error reading charmm36 to martini mapping for TOCL2 (file: /home/eduardo/bilayer/cg-to-aa/Mapping/asn.amber.map).
Error reading slipids to martini mapping for TOCL2 (file: /home/eduardo/bilayer/cg-to-aa/Mapping/asn.amber.map).
Error reading amber to martini mapping for TOCL2 (file: /home/eduardo/bilayer/cg-to-aa/Mapping/asn.amber.map).
Error reading charmm27 to martini mapping for DOPG (file: /home/eduardo/bilayer/cg-to-aa/Mapping/dppc.gromos.map).
Error reading charmm36 to martini mapping for DOPG (file: /home/eduardo/bilayer/cg-to-aa/Mapping/dppc.gromos.map).
Error reading slipids to martini mapping for DOPG (file: /home/eduardo/bilayer/cg-to-aa/Mapping/dppc.gromos.map).
Error reading amber to martini mapping for DOPG (file: /home/eduardo/bilayer/cg-to-aa/Mapping/dppc.gromos.map).
Error reading charmm27 to martini mapping for DOPE (file: /home/eduardo/bilayer/cg-to-aa/Mapping/phe.charmm36.map).
Error reading charmm36 to martini mapping for DOPE (file: /home/eduardo/bilayer/cg-to-aa/Mapping/phe.charmm36.map).
Error reading slipids to martini mapping for DOPE (file: /home/eduardo/bilayer/cg-to-aa/Mapping/phe.charmm36.map).
Error reading amber to martini mapping for DOPE (file: /home/eduardo/bilayer/cg-to-aa/Mapping/phe.charmm36.map).
Residues defined for transformation from martini to gromos54a7:
dict_keys()
None
gmx grompp -f 1-EM.mdp -c 0-backward.gro -n backmapped.ndx -p backmapped.top -o 1-EM -maxwarn 2
:-) GROMACS - gmx grompp, 2016.4 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof
Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund
Teemu Murtola Szilard Pall Sander Pronk Roland Schulz
Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2017, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx grompp, version 2016.4
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /home/eduardo/bilayer/cg-to-aa
Command line:
gmx grompp -f 1-EM.mdp -c 0-backward.gro -n backmapped.ndx -p backmapped.top -o 1-EM -maxwarn 2
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4#
NOTE 1 : The group cutoff scheme is deprecated since GROMACS 5.0 and will be removed in a future release when all interaction forms are supported for the verlet scheme. The verlet scheme already scales better, and it is compatible with GPUs and other accelerators. Setting the LD random seed to -83912630 Generated 840 of the 2415 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 3 bonded neighbours molecule type 'Protein_chain_B' Excluding 3 bonded neighbours molecule type 'DPPC' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 2 [file backmapped.top, line 52]: System has non-zero total charge: 21.999999 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. ------------------------------------------------------- Program: gmx grompp, version 2016.4 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 612) Fatal error: number of coordinates in coordinate file (0-backward.gro, 64684) does not match topology (backmapped.top, 71084) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -------------------------------------------------------[file 1-EM.mdp]:
The group cutoff scheme is deprecated since GROMACS 5.0 and will be
removed in a future release when all interaction forms are supported for
the verlet scheme. The verlet scheme already scales better, and it is
compatible with GPUs and other accelerators.
Setting the LD random seed to -83912630
Generated 840 of the 2415 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
Excluding 3 bonded neighbours molecule type 'DPPC'
Excluding 2 bonded neighbours molecule type 'SOL'
NOTE 2 : System has non-zero total charge: 21.999999 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. ------------------------------------------------------- Program: gmx grompp, version 2016.4 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 612) Fatal error: number of coordinates in coordinate file (0-backward.gro, 64684) does not match topology (backmapped.top, 71084) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -------------------------------------------------------[file backmapped.top, line 52]:
System has non-zero total charge: 21.999999
Total charge should normally be an integer. See
www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
Program: gmx grompp, version 2016.4
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 612)
Fatal error:
number of coordinates in coordinate file (0-backward.gro, 64684)
does not match topology (backmapped.top, 71084)
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors
My system is composed of a protein dimer (each domain with 131 residues) and 128 dppc molecules with water as solvent. A build the system with the dppc molecules placed randomly in the box and performed a 30 ns simulation with martini force field. Now I'm having problems in backmapping the system to all atom. I built the atomistic target topology using a extended version of the gromos54a7 force field that includes parameters for lipids. When I execute initram-v5.sh something weird happens. The 0-backward.gro generated in the first step misses all of the dppc molecules while the backmapped.top has, as expected, the 128 dppc molecules. The problem then arises when the scripts tries to execute the grompp for performing energy minimization, once topology and coordinate files doesn't have the same amount of atoms.
If anyone knows what I'm doing wrong I would appreciate the advice.
Here is the output of the failed initram-v5.sh execution:
initram.sh version 0.1:
(c)2013 Tsjerk A. Wassenaar, PhD
University of Calgary
2500 University Drive NW
Calgary, Alberta
Canada, T2N 1N4
Now executing...
./initram-v5.sh -f dynamics2.gro -p topol.top -po backmapped.top -o backmapped.gro -from martini -to gromos54a7
Checking dependencies:
backward.py ... /home/eduardo/bilayer/cg-to-aa/backward.py
gmx ... /usr/local/gromacs/bin/gmx
/home/eduardo/bilayer/cg-to-aa/backward.py -f dynamics2.gro -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p topol.top -po backmapped.top -n backmapped.ndx -from martini -to gromos54a7
Error reading charmm27 to martini mapping for POPG (file: /home/eduardo/bilayer/cg-to-aa/Mapping/popc.charmm36.map).
Error reading charmm36 to martini mapping for POPG (file: /home/eduardo/bilayer/cg-to-aa/Mapping/popc.charmm36.map).
Error reading slipids to martini mapping for POPG (file: /home/eduardo/bilayer/cg-to-aa/Mapping/popc.charmm36.map).
Error reading amber to martini mapping for POPG (file: /home/eduardo/bilayer/cg-to-aa/Mapping/popc.charmm36.map).
Error reading charmm27 to martini mapping for TOCL2 (file: /home/eduardo/bilayer/cg-to-aa/Mapping/asn.amber.map).
Error reading charmm36 to martini mapping for TOCL2 (file: /home/eduardo/bilayer/cg-to-aa/Mapping/asn.amber.map).
Error reading slipids to martini mapping for TOCL2 (file: /home/eduardo/bilayer/cg-to-aa/Mapping/asn.amber.map).
Error reading amber to martini mapping for TOCL2 (file: /home/eduardo/bilayer/cg-to-aa/Mapping/asn.amber.map).
Error reading charmm27 to martini mapping for DOPG (file: /home/eduardo/bilayer/cg-to-aa/Mapping/dppc.gromos.map).
Error reading charmm36 to martini mapping for DOPG (file: /home/eduardo/bilayer/cg-to-aa/Mapping/dppc.gromos.map).
Error reading slipids to martini mapping for DOPG (file: /home/eduardo/bilayer/cg-to-aa/Mapping/dppc.gromos.map).
Error reading amber to martini mapping for DOPG (file: /home/eduardo/bilayer/cg-to-aa/Mapping/dppc.gromos.map).
Error reading charmm27 to martini mapping for DOPE (file: /home/eduardo/bilayer/cg-to-aa/Mapping/phe.charmm36.map).
Error reading charmm36 to martini mapping for DOPE (file: /home/eduardo/bilayer/cg-to-aa/Mapping/phe.charmm36.map).
Error reading slipids to martini mapping for DOPE (file: /home/eduardo/bilayer/cg-to-aa/Mapping/phe.charmm36.map).
Error reading amber to martini mapping for DOPE (file: /home/eduardo/bilayer/cg-to-aa/Mapping/phe.charmm36.map).
Residues defined for transformation from martini to gromos54a7:
dict_keys()
None
gmx grompp -f 1-EM.mdp -c 0-backward.gro -n backmapped.ndx -p backmapped.top -o 1-EM -maxwarn 2
:-) GROMACS - gmx grompp, 2016.4 (-:
GROMACS is written by:
Emile Apol Rossen Apostolov Herman J.C. Berendsen Par Bjelkmar
Aldert van Buuren Rudi van Drunen Anton Feenstra Gerrit Groenhof
Christoph Junghans Anca Hamuraru Vincent Hindriksen Dimitrios Karkoulis
Peter Kasson Jiri Kraus Carsten Kutzner Per Larsson
Justin A. Lemkul Magnus Lundborg Pieter Meulenhoff Erik Marklund
Teemu Murtola Szilard Pall Sander Pronk Roland Schulz
Alexey Shvetsov Michael Shirts Alfons Sijbers Peter Tieleman
Teemu Virolainen Christian Wennberg Maarten Wolf
and the project leaders:
Mark Abraham, Berk Hess, Erik Lindahl, and David van der Spoel
Copyright (c) 1991-2000, University of Groningen, The Netherlands.
Copyright (c) 2001-2017, The GROMACS development team at
Uppsala University, Stockholm University and
the Royal Institute of Technology, Sweden.
check out www.gromacs.org for more information.
GROMACS is free software; you can redistribute it and/or modify it
under the terms of the GNU Lesser General Public License
as published by the Free Software Foundation; either version 2.1
of the License, or (at your option) any later version.
GROMACS: gmx grompp, version 2016.4
Executable: /usr/local/gromacs/bin/gmx
Data prefix: /usr/local/gromacs
Working dir: /home/eduardo/bilayer/cg-to-aa
Command line:
gmx grompp -f 1-EM.mdp -c 0-backward.gro -n backmapped.ndx -p backmapped.top -o 1-EM -maxwarn 2
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.4#
NOTE 1 : The group cutoff scheme is deprecated since GROMACS 5.0 and will be removed in a future release when all interaction forms are supported for the verlet scheme. The verlet scheme already scales better, and it is compatible with GPUs and other accelerators. Setting the LD random seed to -83912630 Generated 840 of the 2415 non-bonded parameter combinations Excluding 3 bonded neighbours molecule type 'Protein_chain_A' Excluding 3 bonded neighbours molecule type 'Protein_chain_B' Excluding 3 bonded neighbours molecule type 'DPPC' Excluding 2 bonded neighbours molecule type 'SOL' NOTE 2 [file backmapped.top, line 52]: System has non-zero total charge: 21.999999 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. ------------------------------------------------------- Program: gmx grompp, version 2016.4 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 612) Fatal error: number of coordinates in coordinate file (0-backward.gro, 64684) does not match topology (backmapped.top, 71084) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -------------------------------------------------------[file 1-EM.mdp]:
The group cutoff scheme is deprecated since GROMACS 5.0 and will be
removed in a future release when all interaction forms are supported for
the verlet scheme. The verlet scheme already scales better, and it is
compatible with GPUs and other accelerators.
Setting the LD random seed to -83912630
Generated 840 of the 2415 non-bonded parameter combinations
Excluding 3 bonded neighbours molecule type 'Protein_chain_A'
Excluding 3 bonded neighbours molecule type 'Protein_chain_B'
Excluding 3 bonded neighbours molecule type 'DPPC'
Excluding 2 bonded neighbours molecule type 'SOL'
NOTE 2 : System has non-zero total charge: 21.999999 Total charge should normally be an integer. See http://www.gromacs.org/Documentation/Floating_Point_Arithmetic for discussion on how close it should be to an integer. ------------------------------------------------------- Program: gmx grompp, version 2016.4 Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 612) Fatal error: number of coordinates in coordinate file (0-backward.gro, 64684) does not match topology (backmapped.top, 71084) For more information and tips for troubleshooting, please check the GROMACS website at http://www.gromacs.org/Documentation/Errors -------------------------------------------------------[file backmapped.top, line 52]:
System has non-zero total charge: 21.999999
Total charge should normally be an integer. See
www.gromacs.org/Documentation/Floating_Point_Arithmetic
for discussion on how close it should be to an integer.
Program: gmx grompp, version 2016.4
Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 612)
Fatal error:
number of coordinates in coordinate file (0-backward.gro, 64684)
does not match topology (backmapped.top, 71084)
For more information and tips for troubleshooting, please check the GROMACS
website at www.gromacs.org/Documentation/Errors
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- riccardo
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4 years 6 months ago #8284
by riccardo
Replied by riccardo on topic Problems in converting coarse grained to all atom
How many/Which lipids do you have in the system? Is there a mapping available in the Mapping directory for each lipid for your extended gromos force field version?
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- Diniz
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4 years 6 months ago #8286
by Diniz
Replied by Diniz on topic Problems in converting coarse grained to all atom
Hi, I've used only dppc as the phospholipid. In the Mapping directory there is the dppc.gromos.map file, which I think is the required file for this molecule. I've checked that the number of atoms for the gromos model indicated in this map file for dppc is equal to the number of atoms defined for dppc in the topology file (50 atoms). Atom types in the map files don't seem to be the same as the ones defined in the topologies, but I thinks this won't interfere once the protein is recovered in the 0-backward.gro file.
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- tsjerk
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4 years 6 months ago #8287
by tsjerk
Replied by tsjerk on topic Problems in converting coarse grained to all atom
Please try the version of backward at
github.com/Tsjerk/Backward
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- tsjerk
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4 years 6 months ago #8288
by tsjerk
Replied by tsjerk on topic Problems in converting coarse grained to all atom
Please try the version of backward at
github.com/Tsjerk/Backward
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