Hi, Ruth
Are you using the latest Amber16 with newest updates. If so, the format to
apply SMD has been changed to &namelist style, also the variable infe=1
needs to be defined inside &cntrl
you can check this manual for details
http://ambermd.org/doc12/nfe.pdf
Best
Feng
On Thu, Nov 17, 2016 at 5:45 AM, Ruth Helena Tichauer <rhtichau.laas.fr>
wrote:
> Dear Amber users,
>
> I’ve been trying to run SMD of a protein with its ligand in explicit
> solvent using as variable type the Linear Combination Of Distances.
> Although the run has finished with no error messages, the output_file
> (nat1_smd.txt) is not written. Here is my input file:
>
> NCSU steered MD : LCOD rxn coord
> &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=50000, dt=0.001,
> ntpr=25, ntwx=50, ntwr=100, ioutfm=1,
> ntc=2, ntf=2,
> noshakemask = '.2828-2851,2931-2936,5394-5396',
> ntr=1,
> restraintmask = ':170,185,.CA,C,N',
> restraint_wt=5.0,
> ifqnt=1,
> /
> &qmmm
> qmmask = ':179,186-187,1007',
> qmcharge=-1,
> qm_theory='PM3',
> qmshake=0,
> qmcut=8.0,
> /
>
> ncsu_smd
> output_file = ‘nat1_smd.txt'
> output_freq = 50
>
> variable
> type = LCOD
> i = (5394,5395,2649,5395)
> r = (1.0,-1.0)
> path = (0.9,-0.9)
> harm = (1000.0)
> end variable
>
> end ncsu_smd
>
> To check out, I’ve tried to do the same kind of simulation following the
> corresponding tutorial (A10) and again, although the run finishes smoothly,
> with no errors and an effective proton transfer, the output_file (smd.txt)
> is not written. This is the command I used to launch the calculation using
> the provided files:
>
> $AMBERHOME/bin/sander -i mdin -p mr.top -c mr_eq.rst -o mr_pd.out -r
> mr_pd.rst -x mr_pd.nc &
>
> I wonder if I’m missing something from the tutorial.
>
> I’m using Ambertools and Amber 16.
>
> Thank you for any suggestion on this matter,
>
> Sincerely,
>
> Ruth
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Feng Pan
Ph.D. Candidate
North Carolina State University
Department of Physics
Email: fpan3.ncsu.edu
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Received on Thu Nov 17 2016 - 09:30:02 PST
