Hi there,
I’m having some trouble calculating the energy of a small molecule in the gas phase using cpptraj via the sander API (“esander” command).
The default behavior seems to add in the generalized Born term, so I tried adding “igb 0” to the “esander” command line. This leads to the following error message (below).
I checked the source code and the error seems to be in a function called check_prime_factors, which seems to be unrelated to what I’m trying to do. I understand I can use the “energy” command for my simple gas-phase system, but I’d rather it come from sander because that’s the “reference implementation” for lack of a better term.
Please let me know what you think.
Thanks,
- Lee-Ping
Input:
> parm amber.prmtop
> trajin amber-md.netcdf
> esander ENERGIES out esander.txt igb 0
Output:
> BEGIN TRAJECTORY PROCESSING:
> .....................................................
> ACTION SETUP FOR PARM 'amber.prmtop' (1 actions):
> 0: [esander ENERGIES out esander.txt igb 0]
> ----- amber-md.netcdf (1-2000, 1) -----
> Writing topology 0 (amber.prmtop) to 'CpptrajEsander.parm7' with format Amber Topology
> Warning: 'ntb' not specified; setting to 0 based on box type 'None'
> Warning: 'cut' not specified; setting to 9999.0 based on 'ntb'
> SANDER INPUT OPTIONS:
> extdiel= 78.50 intdiel= 1.00 rgbmax= 25.00 saltcon= 0.00 cut= 9999.00
> dielc= 1.00 rdt= 0.00 fswitch= -1.00 igb= 0 alpb= 0
> gbsa= 0 ntb= 0 lj1264= -1 ipb= 0 inp= 2
> vdwmeth= 1 ew_type= 0 ifqnt= 0 jfastw= 0 ntf= 2
> ntc= 2
> ASSERTion ' n > 0 ' failed in ew_setup.F90 at line 306.
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Received on Mon Feb 12 2018 - 14:30:02 PST
