Dear AMBER users,
I’m trying to perform a SMD simulation of a protein with its ligand. I’m treating quantum mechanically the ligand, three water molecules present in the active site, a Mg2+ ion and a few residues of the protein.
I’ve previously minimised and equilibrated the system treating quantum mechanically the same atoms/residues.
Yet, I keep getting the following error message that didn’t appear when I was running a “regular” QM/MM MD:
Error in group input::atommask.f::selectElemMask
elementary mask does not start with : or .
Here is the input file:
&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=1000, dt=0.001,
ntpr=10, ntwx=10, ntwr=100,
ntc=2, ntf=2,
noshakemask = '.474-494,521-534,900-909,917-933,2646-2689,2828-2851,2931-2936,5394-5396,9369-9371',
ntr=1,
restraintmask = ':170,185,&CA,C,N',
restraint_wt=5.0,
ifqnt=1, jar=1,
/
&qmmm
qmmask = ':32,35,59,61,168,169,179,186-187,1007,2332',
qmcharge=-1,
qm_theory='PM3',
qmshake=0,
qmcut=12.0,
/
&wt type='DUMPFREQ', istep1=1, /
&wt type='END', /
DISANG=dist-nat1.RST
DUMPAVE=dist_vs_t-nat1
LISTIN=POUT
LISTOUT=POUT
I’m using amber11 (I should get the latest version of amber and ambertools any time but for now I have to stick with this version).
Thank you for any suggestion (as I don’t manage to see my mistake),
Ruth
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Received on Mon Feb 08 2016 - 06:00:05 PST
