backward job failed
- albumns
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6 years 6 months ago - 6 years 6 months ago #7402
by albumns
backward job failed was created by albumns
Hello,
I am trying to convert my cg system to all-atom with following command line:
but it always failed with messages:
Here is my all-atom topol.top:
I am trying to convert my cg system to all-atom with following command line:
backward-v5/cg> sh initram-v5.sh -f comp1-lipid.gro -p topol-all.top -np 8 -from martini -to CHARMM36
but it always failed with messages:
Checking dependencies: backward.py ... /home/albert/install/gromacs/5.1.4/bin/backward.py gmx ... /home/albert/install/gromacs/5.1.4/bin/gmx /home/albert/Desktop/Imp/cg/backward-v5/cg/backward.py -f comp1-lipid.gro -raw projected.gro -o 0-backward.gro -kick 0.05 -sol -p topol-all.top -po backmapped.top -n backmapped.ndx -from martini -to CHARMM36 Traceback (most recent call last): File "/home/albert/Desktop/Imp/cg/backward-v5/cg/backward.py", line 638, in <module> top = options["-p"] and Topology(options["-p"].value,out=options["-pp"].value) File "/home/albert/Desktop/Imp/cg/backward-v5/cg/backward.py", line 543, in __init__ self.atoms = [[a,r,i,c,0,0,0,t] for t,c in mr for a,r,i,m in self.moleculetypes[t]] KeyError: 'SOL'
Here is my all-atom topol.top:
; Include forcefield parameters #include "charmm36-jul2017.ff/forcefield.itp" #include "POPC.itp" ; Include chain topologies #include "topol_Protein_chain_A.itp" #include "topol_Protein_chain_B.itp" #include "topol_Protein_chain_C.itp" #include "topol_Protein_chain_D.itp" ; Include water topology #include "charmm36-jul2017.ff/tip3p.itp" #ifdef POSRES_WATER ; Position restraint for each water oxygen [ position_restraints ] ; i funct fcx fcy fcz 1 1 1000 1000 1000 #endif ; Include topology for ions #include "charmm36-jul2017.ff/ions.itp" [ system ] ; Name Protein [ molecules ] ; Compound #mols Protein_chain_A 1 Protein_chain_B 1 Protein_chain_C 1 Protein_chain_D 1 POPC 597 POPC 543 SOL 34150 NA+ 376 CL- 376
Last edit: 6 years 6 months ago by albumns.
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- riccardo
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6 years 6 months ago - 6 years 6 months ago #7403
by riccardo
Replied by riccardo on topic backward job failed
Wild guess from:
KeyError: 'SOL'
do you have a mapping file for the water (e.g., sol.charmm36.map)?
KeyError: 'SOL'
do you have a mapping file for the water (e.g., sol.charmm36.map)?
Last edit: 6 years 6 months ago by riccardo.
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- albumns
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6 years 6 months ago #7404
by albumns
Replied by albumns on topic backward job failed
I don't know. Here is all I have in the mapping directory:
a.charmm36.map dat3.charmm36.map dt.charmm36.map ile.charmm36.map trp.charmm36.map
ala.charmm36.map dat5.charmm36.map dtt3.charmm36.map leu.charmm36.map tyr.charmm36.map
arg.charmm36.map dc.charmm36.map dtt5.charmm36.map lys.charmm36.map u.charmm36.map
asn.charmm36.map dct3.charmm36.map g.charmm36.map met.charmm36.map val.charmm36.map
asp.charmm36.map dct5.charmm36.map gln.charmm36.map phe.charmm36.map
c.charmm36.map dg.charmm36.map glu.charmm36.map pro.charmm36.map
cys.charmm36.map dgt3.charmm36.map gly.charmm36.map ser.charmm36.map
da.charmm36.map dgt5.charmm36.map his.charmm36.map thr.charmm36.map
a.charmm36.map dat3.charmm36.map dt.charmm36.map ile.charmm36.map trp.charmm36.map
ala.charmm36.map dat5.charmm36.map dtt3.charmm36.map leu.charmm36.map tyr.charmm36.map
arg.charmm36.map dc.charmm36.map dtt5.charmm36.map lys.charmm36.map u.charmm36.map
asn.charmm36.map dct3.charmm36.map g.charmm36.map met.charmm36.map val.charmm36.map
asp.charmm36.map dct5.charmm36.map gln.charmm36.map phe.charmm36.map
c.charmm36.map dg.charmm36.map glu.charmm36.map pro.charmm36.map
cys.charmm36.map dgt3.charmm36.map gly.charmm36.map ser.charmm36.map
da.charmm36.map dgt5.charmm36.map his.charmm36.map thr.charmm36.map
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- riccardo
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6 years 6 months ago #7405
by riccardo
Replied by riccardo on topic backward job failed
Hold on, from the
backward tutorial pagetutorial page
I read:
Note, water and ions can be skipped in the .top files as they are automatically detected by backward.py.
Just try to remove the water and ions from the TOP file and run the initram.sh command once more.
Note, water and ions can be skipped in the .top files as they are automatically detected by backward.py.
Just try to remove the water and ions from the TOP file and run the initram.sh command once more.
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