Dear Diego,
Thanks for your quick response, I really appreciate it.
I understand what you wrote, I'm going to test it!
Thanks,
Sonia.
2017-07-19 15:23 GMT+02:00 <diego.soler.uam.es>:
> Hi Sonia,
>
> Use an umbrella potential with a large enough force constant. I've
> done it quite a few times by using an input file and a restraint file
> which I attach below:
>
> Input File:
>
> QM/MM min
> &cntrl
> nmropt = 1, ntx = 1, irest = 0,
> ntrx = 1, ntxo = 1,
> ntpr = 1, ntwx = 1, ntr = 0,
> ntf = 1, ntb = 0, ntc=1,
> cut = 9999,
> imin = 1, maxcyc = 100, ncyc = 100,
> nstlim = 100,
> ifqnt = 1
> /
> &qmmm
> qmmask= ':1,2'
> qm_theory='fireball',
> qm_ewald= 0,
> qmcharge= 0,
> writepdb= 1,
> printcharges= 1,
> qmshake= 0,
> itrmax= 70,
> fb_iqout=3,
> &wt type='END' &end
> DISANG= rst.dat
> LISTOUT= rst.lis
>
> And the auxiliary file (rst.dat):
>
> ######################
> # distancia N1-H1
> ######################
> &rst iat=1,1,
> iresid=1, ifvari=0,
> atnam(1)='N1', atnam(2)='H1'
> r1=0.000, r2=1.0775, r3=1.0775, r4=10,
> rk2=20000, rk3=20000,
> &end
> ######################
>
> This worked perfectly fine for me.
>
> Best,
>
> Diego Soler Polo
>
>
>
>
>
>
>
>
>
>
>
> Quoting Sonia Romero <sromerte11.gmail.com>:
>
> > Dear all,
> >
> > I'm trying to perform a qm/mm minimization of a protein with its ligand
> in
> > the active site.
> > However, it is essential for me to mantain a distance fixed, which
> involves
> > the ligand and an hydrogen from one of the residues in the qm region:
> >
> > I'm wondering if it is possible to have restraints between two atoms
> which
> > are in the qm region, since I've been trying it and I'm not succeding.
> >
> > Here is my input:
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > *min &cntrl imin = 1, ncyc = 500, maxcyc = 1000, ntmin=1, irest=0,
> > ntx=1, ntb=1,*
> >
> > * nmropt=1,*
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> >
> > * cut = 12.0, restraintmask=':427.C1 >:15', restraint_wt=1000,
> > ifqnt=1,/&qmmm qmmask='.2509-2518,5215-5223,6716-6759', qmcharge=-1,
> > spin=1, qm_theory='DFTB', dftb_3rd_order='PA', qmshake=0, qm_ewald=1,
> > writepdb=1,&end&wt type='END' /DISANG=restraint_file*
> > where the restraint_file is
> >
> >
> >
> > *&rst restraint="distance(:161.HE2, :428.O4D)",&end*
> >
> > As I said before both 161.HE2 and 428.O4D are in the qm region.
> >
> > I've also tried to use the program makeDIST_RST with the order
> >
> >
> >
> > *makeDIST_RST -upb 7col.dist -pdb coords_opt_282pbe.pdb -rst RST.dist*
> > where 7col.dist is:
> >
> >
> >
> > *161 GLH HE2 428 PNP O4D 2.0*
> > But I obtain an error message:
> >
> >
> >
> >
> >
> >
> > *# makeDIST_RSTCurrently configured for up to 50000 atomsUsing MAP file
> > /sharelab/labapps/CENTOS7/AMBER/amber16/dat/map.DG-AMBERERROR no map
> > function for HE2 GLH :data= 161 GLH HE2 428 PNP O4D 2.0*
> > that's why I read the manual and found the alternative
> reatraint=distance()
> > option.
> >
> > I will really appreaciate any help,
> >
> > Thank you in advance
> >
> >
> > Sonia
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
>
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Received on Wed Jul 19 2017 - 07:30:03 PDT
