Christopher G Jesudason
formerly
Chemistry Department
University of Malaya
50603 Kuala Lumpur
Malaysia
Residence:
24, Jalan. 2/132
Taman Gasing Indah,
59200 Kuala Lumpur,
Malaysia
tel: (h/p) 016-341-5157
On Sun, Apr 12, 2026, 7:25 AM Goetz, Andreas via AMBER <amber.ambermd.org>
wrote:
> Dear Dr Radwan,
>
> The namelist for using GAMESS is &gms (not &gamess) and the namelist
> variables you have in your input file (qm_external_type,
> qm_external_options, gamess_path) do not exist. Please check the Amber
> manual.
>
> I also recommend to first check whether the test in
> $AMBERHOME/test/qmmm_EXTERN/pure_QM_MD_GAMESS works.
>
> All the best,
> Andy
> —
> Dr. Andreas W. Goetz
> Associate Research Scientist
> San Diego Supercomputer Center
> Tel: +1-858-822-4771
> Email: agoetz.sdsc.edu
> Web: www.awgoetz.de
>
> On Apr 11, 2026, at 2:09 AM, A R via AMBER <amber.ambermd.org> wrote:
>
> Dear ALL
> Good day
> Could you please help and fix the following sander input file (Amber24).
> Prod-qmmm.in
> QM/MM DFT Production - 2NO9
> &cntrl
> imin=0, ntx=5, irest=1,
> nstlim=100000, dt=0.001,
> ntb=1, ntc=2, ntf=2,
> cut=8.0, temp0=300.0, ntt=3, gamma_ln=2.0,
> ntr=1, restraintmask=':1-242', restraint_wt=0.1,
> ifqnt=1,
> /
> &qmmm
> qmmask=':243,244',
> qmcharge=-3,
> qm_theory='EXTERN',
> qm_ewald=0,
> /
> &gamess
> qm_external_type='GAMESS',
> qm_external_options='GBASIS=N31 NGAUSS=6 DFTTYP=B3LYP',
> gamess_path='/home/aradwan/gamess/rungms',
> /
>
>
>
> prod-qmmm.out
> Also, this is the bottom section of the output file:
> QMMM: 62 4050 H 2.8315 -4.7470 -3.4315
> QMMM: 63 4051 H 1.8051 -6.6739 -2.5007
> QMMM: 64 4052 H 5.5400 -11.1814 1.2638
> QMMM: 65 4053 H 4.4820 -7.9490 -1.7316
>
>
> --------------------------------------------------------------------------------
> 3.1 QM CALCULATION INFO
>
> --------------------------------------------------------------------------------
>
> | Please also cite the following work for the use of the QM/MM interface:
>
> | A. W. G"otz, M. A. Clark, R. C. Walker
> | "An extensible interface for ab initio QM/MM molecular dynamics
> simulations
> | with AMBER"
> | J. Comput. Chem. 35 (2014) 95-108.
> | DOI: 10.1002/jcc.23444
>
> Constants for unit conversion taken from
> Mohr, Taylor, Newell, Rev. Mod. Phys. 80 (2008) 633-730
> and using the thermochemical calorie (1 cal = 4.184 J):
>
> A_TO_BOHRS = 1.889726132873E+00
> AU_TO_KCAL = 6.2750946943E+02
> AU_TO_DEBYE = 2.54174623E+00
> SANDER BOMB in subroutine qm2_extern_get_qm_forces
> External namelist not found
> Please check your input.
> "prod_qmmm.out"
>
>
> Best regards
>
> Sincerely yours'
>
> Professor, Ph.D, (Full) Dr. Awwad A. Radwan
> (Current address: Pharmaceutical Technology center, Fac of Pharmacy, King
> Saud University, Al Ryiadh, Kingdom of Saudi Arabia, Office :
> +966-046-70562 Mob. 0505193925)
>
> (Home country address: Dept of Org Pharm Chemistry, Faculty of Pharmacy,
> Assiut University, Assiut, Egypt. Home Tel +2088-292164 Office Tel
> +2088-411326 Fax +2088-332776 Mobile 0103-716131)
>
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Received on Sat Apr 11 2026 - 19:30:02 PDT
