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