iqmatoms is NOT a mask. It is a sequence of integers. Do not put any
quotes or mask-style symbols (., :, etc.). Just put the list of qm atoms
that you want added. All of this is described in the manual.
Hope this helps,
Jason
On Fri, Mar 25, 2011 at 3:21 PM, Mahmoud Soliman <mahmoudelkot.gmail.com>wrote:
>
> Hi Amber experts,
> I am running QM/MM for ligand-enzyme complex but I keep getting the
> following error. The input job is also shown below.. Any help would be
> appreciated
> Bad data for namelist object iqmatoms
> Bad data for namelist object iqmatoms
> Bad data for namelist object iqmatoms
> Cannot match namelist object name ’pm3’,
> qmcut
> namelist read: missplaced = sign
> Cannot match namelist object name .0,
> Job input
> =======
> QM/MM free equilibration NPT
> &cntrl
> imin = 0,
> irest = 0,
> ntx = 7,
> ntb = 2,
> pres0 = 1.0,
> ntp = 1,
> taup = 2,
> cut = 10,
> ntr =0,
> tempi = 300.0, temp0 = 300.0,
> ntc=2,
> ntf=2,
> ntr = 0,
> ntt = 3,
> gamma_ln = 1.0,
> nstlim =50000, dt = 0.002,
> ntpr = 500, ntwx = 500, ntwr = 500, ntwe = 500,
> ifqnt=1,
> /
> &qmmm
> iqmatoms='2790-2818, 2581-2587, 1132-1137',
> qmcharge=-1,
> qm_theory=’PM3’,
> qmcut=8.0,
> /
> Thanks
> Mahmoud
> _______________________________________________
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri Mar 25 2011 - 16:00:02 PDT
