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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Feb 08 2018 - 13:00:03 PST
