Hi Ruth,
The error message in sander just states that Orca did not produce a valid output file, i.e. something went wrong during the execution of Orca. From what you describe, it does sound like sander wrote an invalid input file for Orca. You said that you have tested the setup for you system before and it worked - can you confirm that your sander input file is indeed identical to your previous tests that worked? Does QM/MM with an internal QM method work? What happens if you switch off smd?
All the best,
Andy
—
Dr. Andreas W. Goetz
Assistant Research Scientist
San Diego Supercomputer Center
Tel: +1-858-822-4771
Email: agoetz.sdsc.edu
Web: www.awgoetz.de
> On Feb 8, 2018, at 3:37 PM, Ruth Helena Tichauer <rhtichau.laas.fr> wrote:
>
> Dear Amber users,
>
> I’m trying to run a SMD simulation of a protein-ligand complex in explicit solvent using the following input file:
>
> SMD LCOD rxn coord using Orca
> &cntrl
> imin=0,
> irest=1, ntx=5,
> ntb=2, pres0=1.0, ntp=1, taup=1.0,
> cut=12.0,
> tempi=300.0, temp0=300.0,
> ntt=3, gamma_ln=2.0, ig=-1,
> nstlim=100000, dt=0.0005,
> ntpr=100, ntwx=100, ntwr=1000, ioutfm=1,
> ntc=2, ntf=2,
> noshakemask = '.2646-2689,2828-2851,2941-2946,11881-11883,14608-14610',
> ntr=1,
> restraintmask = ':170,185,.CA,C,N',
> restraint_wt=5.0,
> ifqnt=1, infe=1
> /
> &qmmm
> qmmask = ':168,169,179,196-197,3176,4085',
> qmcharge=0,
> qm_theory='EXTERN',
> qmshake=0,
> qmcut=17.0,
> /
> &orc
> method='PBE',
> basis=‘def2-SVP’,
> cbasis=‘def2-SVP’,
> jbasis=‘def2-SVP',
> num_threads=1,
> convkey=’TIGHTSCF’,
> dipole=1,
> maxiter=150,
> /
> &smd
> output_file = 'nat_smdo25-1_198.txt'
> output_freq = 20
> cv_file='cv_nat-1_198.in'
> /
>
> Previously, I was encountering energy convergence problems within Orca and in my last attempt to solve this issue, I took a further minimised structure, solvated it in a 14 A octahedron box, minimised the solvent, heated the system from 0 to 300K. Now that I want to proceed with the SMD, the calculation is not even starting, I got this very odd message that I didn’t get before in the orc_job.dat file:
>
> Error: XYZ File is for simple coordinate input only
> Unknown atom specifier: -2.8123014350914630 0.9725245871287427 0.8684715494137160
> [file orca_tools/Tool-Scanner/qcscancoord.cpp, line 30]:
>
> Apparently somehow Amber is not building “readable” inputs for Orca (?) Which is odd because this was not the case before.. Here is the error message in the amber output file (if useful):
>
> SANDER BOMB in subroutine read_results (qm2_extern_orc_module)
> Error reading Orca output from file orc_job.engrad
> (Current total energy or gradient not found or unsupported units.)
>
> Thank you in advance for any help in solving this issue,
>
> Sincerely,
>
> Ruth
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Received on Thu Feb 08 2018 - 14:00:02 PST
