ValueError: for atom type POT, 0 parameters found (expecting 1, found: [])

[odraccix]

Hi resal81 and everyone,
I had a similar problem to that of krlitros87 (#23).
I have a system composed by a membrane protein in which several ions ( K+, Na+, Cl-) are present both in the selective filter (K+) of the channel protein and in the solvation box (K+, Na+, Cl-).

I'm using par_all36_lipid.prm, par_all36_prot.prm, toppar/toppar_water_ions.str as the parameters file, but it seems that this choice was not good, although it tried to replace K atom type with POT and vice versa.

This is my output..

mainapp - DEBUG - >> started main
mainapp.psf.PSFSystem - DEBUG - >> entering PSFSystem
mainapp.psf.PSFSystem - DEBUG - parsing psf file: sodium.psf
mainapp.psf.PSFSystem - WARNING - could not find NAMD keywork in the first line in the psf file
mainapp.psf.PSFSystem - DEBUG - skipping section: '33 !NTITLE'
mainapp.psf.PSFSystem - DEBUG - skipping section: '0 !NDON: donors'
mainapp.psf.PSFSystem - DEBUG - skipping section: '0 !NACC: acceptors'
mainapp.psf.PSFSystem - DEBUG - skipping section: '0 !NNB'
mainapp.psf.PSFSystem - DEBUG - skipping section: '1 0 !NGRP'
mainapp.psf.PSFSystem - DEBUG - parsing took 7.7 seconds
mainapp.psf.PSFSystem - DEBUG - << leaving PSFSystem
mainapp.psf.PSFSystem - DEBUG - converting psf to multiple molecules based on chains
mainapp.charmmpar.CharmmPar - DEBUG - >> entering CharmmPar
mainapp.charmmpar.CharmmPar - DEBUG - parsing parameter file: par_all36_prot.prm
mainapp.charmmpar.CharmmPar - DEBUG - parsing took 0.0 seconds
mainapp.charmmpar.CharmmPar - DEBUG - 132 bonding, 362 angle, 546 dih, 35 imp, 53 nonbonding and 6 cmaps
mainapp.charmmpar.CharmmPar - DEBUG - parsing parameter file: par_all36_lipid.prm
mainapp.charmmpar.CharmmPar - DEBUG - parsing took 0.0 seconds
mainapp.charmmpar.CharmmPar - DEBUG - 182 bonding, 493 angle, 650 dih, 39 imp, 82 nonbonding and 6 cmaps
mainapp.charmmpar.CharmmPar - DEBUG - parsing parameter file: toppar_water_ions_Matteo_edit.str
mainapp.charmmpar.CharmmPar - DEBUG - parsing took 0.0 seconds
mainapp.charmmpar.CharmmPar - DEBUG - 182 bonding, 493 angle, 650 dih, 39 imp, 82 nonbonding and 6 cmaps
mainapp.charmmpar.CharmmPar - DEBUG - << leaving CharmmPar
mainapp.charmmpar.CharmmPar - DEBUG - adding parameters to the system...
Traceback (most recent call last):
File "psf2top.py", line 107, in
main()
File "psf2top.py", line 96, in main
par.add_params_to_system(psfsys, panic_on_missing_param=True)
File "/usr/local/lib/python2.7/dist-packages/pytopol/parsers/charmmpar.py", line 296, in add_params_to_system
raise ValueError(msg)
ValueError: for atom type POT, 0 parameters found (expecting 1, found: [])

---

Hoping it will be useful to solve the problem... because this issue makes me crazy!!

Thank you in advance

[resal81]

Hi odraccix,

It looks like that your last param file is not parsed correctly:

mainapp.charmmpar.CharmmPar - DEBUG - parsing parameter file: par_all36_prot.prm
mainapp.charmmpar.CharmmPar - DEBUG - parsing took 0.0 seconds
mainapp.charmmpar.CharmmPar - DEBUG - 132 bonding, 362 angle, 546 dih, 35 imp, 53 nonbonding and 6 cmaps
mainapp.charmmpar.CharmmPar - DEBUG - parsing parameter file: par_all36_lipid.prm
mainapp.charmmpar.CharmmPar - DEBUG - parsing took 0.0 seconds
mainapp.charmmpar.CharmmPar - DEBUG - 182 bonding, 493 angle, 650 dih, 39 imp, 82 nonbonding and 6 cmaps
mainapp.charmmpar.CharmmPar - DEBUG - parsing parameter file: toppar_water_ions_Matteo_edit.str
mainapp.charmmpar.CharmmPar - DEBUG - parsing took 0.0 seconds
mainapp.charmmpar.CharmmPar - DEBUG - 182 bonding, 493 angle, 650 dih, 39 imp, 82 nonbonding and 6 cmaps

Note how the number of parameters (i.e. nonbonding, ...) is not changed after reading toppar_water_ions_Matteo_edit.str. One thing you can do is to extract the parameter section of the str file into another file (basically anything between read_para and the final END) and try it out. Hopefully this will solve the problem.