Thanks Jason,
It works fine now!
Best wishes
Mahmoud
On 3/26/11 12:32 AM, Jason Swails wrote:
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 [1]<mahmoudelkot.gmail.com>wro
te:
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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[3]
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--
*************************************************
Mahmoud E. Soliman
Computational Chemistry & Modeling (PhD)
Department of Chemistry
University of Bath
Bath
BA2 7AY
United Kingdom
[4]
http://people.bath.ac.uk/mess20/
[5]
http://www.bath.ac.uk/person/812559
*********************************************
Mahmoud E. Soliman
Lecturer of pharmaceutical organic chemistry
Pharmaceutical Organic Chemistry Dept.
Faculty of pharmacy
Zagazig University
Zagazig
Egypt
**********************************************
Email:
[6]mess20.bath.ac.uk
[7]meelkot.zu.edu.eg
[8]mahmoudelkot.gmail.com
References
1. mailto:mahmoudelkot.gmail.com
2. mailto:AMBER.ambermd.org
3.
http://lists.ambermd.org/mailman/listinfo/amber
4.
http://people.bath.ac.uk/mess20/
5.
http://www.bath.ac.uk/person/812559
6. mailto:mess20.bath.ac.uk
7. mailto:meelkot.zu.edu.eg
8. mailto:mahmoudelkot.gmail.com
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Received on Sun Mar 27 2011 - 23:00:02 PDT
