set qm_theory=1 if you want to use PM3 to treat QM,
Please see more information in AMBER manual
On Fri, Mar 25, 2011 at 6:16 PM, Yuan Yao <yylovely.gmail.com> wrote:
> iqmatoms='.2790-2818, 2581-2587, 1132-1137',
>
> On Fri, Mar 25, 2011 at 6:21 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
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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Received on Fri Mar 25 2011 - 15:30:03 PDT
