normal backward job failed

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2 months 1 week ago - 2 months 1 week ago #7402 by albumns
albumns created the topic: backward job failed
Hello,

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: 2 months 1 week ago by albumns.

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2 months 1 week ago - 2 months 1 week ago #7403 by riccardo
riccardo replied the topic: backward job failed
Wild guess from:

KeyError: 'SOL'

do you have a mapping file for the water (e.g., sol.charmm36.map)?
Last Edit: 2 months 1 week ago by riccardo.

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2 months 1 week ago #7404 by albumns
albumns replied the 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

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2 months 1 week ago #7405 by riccardo
riccardo replied the 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.

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