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Backmapping fails, Martini POPC lipids to charmm36
- z.sichaib
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3 years 7 months ago - 3 years 7 months ago #8727
by z.sichaib
Backmapping fails, Martini POPC lipids to charmm36 was created by z.sichaib
Dear Martini users,
I am trying to backmap a protein with lipids (POPC) from Martini FF to charmm36, using Gromacs 2019.3
The backmapping is giving the following error:
NB1: I took the all-atom topology of POPC (POPC_charmmgui.itp) from Charmm-Gui.
NB2: The backmapping works fine when I backmap the protein alone.
NB3: I tried to do the backmapping using popc.itp + posre_popc.itp from aquaporin tutorial and it also worked fine.
NB4: The difference between popc.itp from aquaporin tutorial and POPC_charmmgui is in the restraints:
Tail of popc.itp (aquaporin tutorial):
; Include Position restraint file
#ifdef POSRES
#include "posre_popc.itp"
#endif
Tail of POPC_charmmgui.itp:
#ifdef POSRES
[ position_restraints ]
20 1 0.0 0.0 POSRES_FC_LIPID
#endif
#ifdef DIHRES
[ dihedral_restraints ]
25 36 28 30 1 -120.0 2.5 DIHRES_FC
60 63 65 67 1 0.0 0.0 DIHRES_FC
#endif
Did someone had a similar error when backmapping lipids from Martini to charmm36 using topologies from Charmm-Gui?
I can't see what is wrong with the line 1272 in the file POPC_charmmgui.itp. Any help, suggestions, please?
I would have used directly topology of POPC from the aquaporin tutorial but I also have other types of lipids to backmap from other systems so, I need to understand what is wrong in the itp file loaded from Charmm-Gui.
Any help would be more than appreciated.
I am trying to backmap a protein with lipids (POPC) from Martini FF to charmm36, using Gromacs 2019.3
The backmapping is giving the following error:
ERROR 1 : Incorrect number of parameters - found 2, expected 3 or 6 for Position Rest. (after the function type).[/quote] [quote]This is what the line 1272 contains: 1270 #ifdef POSRES 1271 [ position_restraints ] 1272 20 1 0.0 0.0 POSRES_FC_LIPID 1273 #endif[/quote] NB1: I took the all-atom topology of POPC (POPC_charmmgui.itp) from Charmm-Gui. NB2: The backmapping works fine when I backmap the protein alone. NB3: I tried to do the backmapping using popc.itp + posre_popc.itp from aquaporin tutorial and it also worked fine. NB4: The difference between popc.itp from aquaporin tutorial and POPC_charmmgui is in the restraints: Tail of popc.itp (aquaporin tutorial): ; Include Position restraint file #ifdef POSRES #include "posre_popc.itp" #endif Tail of POPC_charmmgui.itp: #ifdef POSRES [ position_restraints ] 20 1 0.0 0.0 POSRES_FC_LIPID #endif #ifdef DIHRES [ dihedral_restraints ] 25 36 28 30 1 -120.0 2.5 DIHRES_FC 60 63 65 67 1 0.0 0.0 DIHRES_FC #endif Did someone had a similar error when backmapping lipids from Martini to charmm36 using topologies from Charmm-Gui? I can't see what is wrong with the line 1272 in the file POPC_charmmgui.itp. Any help, suggestions, please? I would have used directly topology of POPC from the aquaporin tutorial but I also have other types of lipids to backmap from other systems so, I need to understand what is wrong in the itp file loaded from Charmm-Gui. Any help would be more than appreciated.[file POPC_charmmgui.itp, line 1272]:
Incorrect number of parameters - found 2, expected 3 or 6 for Position Rest. (after the function type).
This is what the line 1272 contains:
1270 #ifdef POSRES
1271 [ position_restraints ]
1272 20 1 0.0 0.0 POSRES_FC_LIPID
1273 #endif
NB1: I took the all-atom topology of POPC (POPC_charmmgui.itp) from Charmm-Gui.
NB2: The backmapping works fine when I backmap the protein alone.
NB3: I tried to do the backmapping using popc.itp + posre_popc.itp from aquaporin tutorial and it also worked fine.
NB4: The difference between popc.itp from aquaporin tutorial and POPC_charmmgui is in the restraints:
Tail of popc.itp (aquaporin tutorial):
; Include Position restraint file
#ifdef POSRES
#include "posre_popc.itp"
#endif
Tail of POPC_charmmgui.itp:
#ifdef POSRES
[ position_restraints ]
20 1 0.0 0.0 POSRES_FC_LIPID
#endif
#ifdef DIHRES
[ dihedral_restraints ]
25 36 28 30 1 -120.0 2.5 DIHRES_FC
60 63 65 67 1 0.0 0.0 DIHRES_FC
#endif
Did someone had a similar error when backmapping lipids from Martini to charmm36 using topologies from Charmm-Gui?
I can't see what is wrong with the line 1272 in the file POPC_charmmgui.itp. Any help, suggestions, please?
I would have used directly topology of POPC from the aquaporin tutorial but I also have other types of lipids to backmap from other systems so, I need to understand what is wrong in the itp file loaded from Charmm-Gui.
Any help would be more than appreciated.
Last edit: 3 years 7 months ago by z.sichaib.
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- Posts: 43
3 years 6 months ago #8732
by z.sichaib
Replied by z.sichaib on topic Backmapping fails, Martini POPC lipids to charmm36
Hi,
I will try to explain my problem here.
The backmapping of POPC from Martini to Charmm36 FF is working fine when I use the AA itp files (popc.itp and posre_popc.itp) from the aquaporin tutorial.
However, when I use AA itp file of POPC from CharmmGUI, I obtain the following error:
ERROR 1 : Incorrect number of parameters - found 2, expected 3 or 6 for Position Rest. (after the function type).
The line in the itp file (POPC.itp from CharmmGUI) that causes the problem has the following:
----
#ifdef POSRES
[ position_restraints ]
1272 20 1 0.0 POSRES_FC_LIPID
#endif
The difference between popc.itp from the aquaporin tutorial and POPC from charmmmGUI is in the restraints:
Tail of popc.itp (aquaporin tutorial):
; Include Position restraint file
#ifdef POSRES
#include "posre_popc.itp"
#endif
Tail of POPC_charmmgui.itp:
#ifdef POSRES
[ position_restraints ]
20 1 0.0 POSRES_FC_LIPID
#endif
#ifdef DIHRES
[ dihedral_restraints ]
25 36 28 30 1 -120.0 2.5 DIHRES_FC
60 63 65 67 1 0.0 0.0 DIHRES_FC
#endif
Did someone had a similar error when backmapping lipids from Martini to charmm36 using topologies from Charmm-Gui?
I can't understand the difference in the restraints between popc.itp from the aquaporin tutorial and the topology file from CharmmGUI? any explanation?
I would have used directly the topology of POPC from the aquaporin tutorial but I also have other types of lipids to backmap from other systems so, I need to understand what is wrong in the itp file loaded from Charmm-Gui. or why backward is throwing the error.
Any help would be more than appreciated.
I will try to explain my problem here.
The backmapping of POPC from Martini to Charmm36 FF is working fine when I use the AA itp files (popc.itp and posre_popc.itp) from the aquaporin tutorial.
However, when I use AA itp file of POPC from CharmmGUI, I obtain the following error:
ERROR 1 : Incorrect number of parameters - found 2, expected 3 or 6 for Position Rest. (after the function type).
The line in the itp file (POPC.itp from CharmmGUI) that causes the problem has the following:
----
#ifdef POSRES
[ position_restraints ]
1272 20 1 0.0 POSRES_FC_LIPID
#endif
The difference between popc.itp from the aquaporin tutorial and POPC from charmmmGUI is in the restraints:
Tail of popc.itp (aquaporin tutorial):
; Include Position restraint file
#ifdef POSRES
#include "posre_popc.itp"
#endif
Tail of POPC_charmmgui.itp:
#ifdef POSRES
[ position_restraints ]
20 1 0.0 POSRES_FC_LIPID
#endif
#ifdef DIHRES
[ dihedral_restraints ]
25 36 28 30 1 -120.0 2.5 DIHRES_FC
60 63 65 67 1 0.0 0.0 DIHRES_FC
#endif
Did someone had a similar error when backmapping lipids from Martini to charmm36 using topologies from Charmm-Gui?
I can't understand the difference in the restraints between popc.itp from the aquaporin tutorial and the topology file from CharmmGUI? any explanation?
I would have used directly the topology of POPC from the aquaporin tutorial but I also have other types of lipids to backmap from other systems so, I need to understand what is wrong in the itp file loaded from Charmm-Gui. or why backward is throwing the error.
Any help would be more than appreciated.
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