search

qcxms / QCxMS

Quantum mechanic mass spectrometry calculation program
https://xtb-docs.readthedocs.io/en/latest/qcxms_doc/qcxms.html
GNU Lesser General Public License v3.0
43 stars 22 forks source link

Deionization of compound after the ground state trajectory #60

Closed 4psireal2 closed 1 year ago

4psireal2 commented 1 year ago

I ran qcxms for the first time and by the second run qcxms, I got this error 

reading qcxms.gs ...
--- Checking QC method for ions ---

 initializing GFN1-xTB ...
 initialization successful!
 energy =      -66.63494
 charge =              1
 mult   =              1
 etemp  =         5000.0
 initializing S=0 state using HS-UHF.
--- QC method okay ---

 *******************************************
       generating randomized ensemble 
 *******************************************
 reading inital coord/velo from qcxms.gs ...
 doing XTB for MO spectrum for M ...
 QM code failure
 prog   =            7
 charge =            0
 mult   =            2
QC initialization error

The coord and qcxms.in input files: coord.txt qcxms.in.txt

tobigithub commented 1 year ago

QCxMS works with two general modes of operation, one for EI-MS (GC-MS) and one for CID-MS/MS (LC-MS/MS). Depending on that you need to choose your input molecule and parameter set.

@psireal9 Your example looks like N-potonated codeine, as [M+H]+ adduct with the molecular formula C18H21NO3+ Meaning you want to calculate the CID-MS/MS? Then you should try with the standard CID-MS/MS settings:

xtb2
cid
elab 60                                                                                                                                
maxcoll 6
noesi

In case you want to calculate the 70eV EI-MS (for GC-MS) spectrum, you need to remove the proton and add the neutral molecule as optimized 3D. image