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
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Received on Wed Jul 19 2017 - 06:30:03 PDT
