1) To make a single molecule from 2 things that are not, I think the easiest
thing to do is use the "bond" command in leap and make a new prmtop. I'd
have to look it up in the manual to tell you exactly how to use it. Leap
may complain if any resulting bond, angle, or dihedral terms are not defined
in your parm.dat file (hence the need for an additional frcmod). Keep in
mind also that this might also affect 1-4 scaling of electrostatics, but I
would assume that your QM region is large enough that this is not a problem.
2) I figured that might happen, but it was worth a shot.
3) This could be done a lot of ways. I would expect the easiest way would
be to use NMR restraints, but I've never used it for that specific purpose.
4)
http://archive.ambermd.org/201109/0156.html
Brian
On Thu, Oct 6, 2011 at 11:42 AM, kaustubh joshi <kandrjoshi.gmail.com>wrote:
> HI
> I initially generated the one molar box , equilibrated it. The
> phenol and imine residues were present randomly in the box. I used one set
> of residues (22,23) to carry out umbrella sampling over the reaction
> coordinate from 12 A to 2.25A. The rst structure I am using now for QMMM
> calculation is one chosen from the MD simulation near the minima on that
> reaction coordinate.
>
> * Could you give guideline on how to set up QM region with these 2 residues
> as one molecule? COuld you share some example?
> * I tried iwrap=0 after your suggestion but that made no change.
> * I got a suggestion to keep one of the molecules in the center (by using
> some condition).Since other molecule is under constraint to be with in
> 2.6 A of the first, the system will stay in the center and this problem
> (which possibly is occuring bcoz of one molecule crossing over the
> boundary and reappearing from other side) can be overcome. But I could
> not find any flag to do so. If you are aware plz. share.
> * Could you give the link to prior thread you started.
>
> Kaustubh
>
> On Thu, Oct 6, 2011 at 5:02 PM, Brian Radak <radak004.umn.edu> wrote:
>
> > Kaustubh,
> >
> > Are the 2 residues wrapping differently? It looks like parts of your QM
> > region might be on opposite sides of the cell (large negative and
> positive
> > coordinates in the lower/upper columns). I think, but am not sure, that
> > using iwrap = 0 would solve that problem.
> >
> > In my QM/MM simulations I usually try to set the QM region as one
> molecule
> > in the prmtop so that it always images together. This requires that all
> of
> > the atoms be bonded together, even if those bonded terms are never used,
> > which is the default behavior for QM/MM anyway. This might also require
> > creating an frcmod with non-standard bonded terms (they can just have 0
> > force constant if you'd like also).
> >
> > I also started a thread several weeks ago while experiencing a similar
> > problem that seemed to be caused by a non-orthorhombic cell. I see that
> > you
> > are using orthorhombic conditions, but that discussion might also be of
> > interest.
> >
> > Regards,
> > Brian
> >
> >
> > On Thu, Oct 6, 2011 at 10:46 AM, kaustubh joshi <kandrjoshi.gmail.com
> > >wrote:
> >
> > > HI ALL!!
> > > I have generated a one molar system with 4 solute
> > > molecules. I have to carry out and umbrella sampling for this system
> > > wherein
> > > a proton is transferred from phenol to the imine. Out of all the
> > > phenol-imine residues present in the system,I am considering residues
> 22
> > > and
> > > 23 for the proton transfer. My problem is the calculations stop with
> > error:
> > >
> > > ERROR: QM region + cutoff larger than box dimension:
> > > QM-MM Cutoff = 4.0000
> > > Coord Lower Upper Size Radius of largest sphere inside
> unit
> > > cell
> > > X -9.745 9.611 19.357 11.528
> > > Y -5.919 11.077 16.996 11.528
> > > Z -12.188 11.060 23.248 11.528
> > > ****************************************************
> > > SANDER BOMB in subroutine QM_CHECK_PERIODIC<qm_mm.f>
> > > QM region + cutoff larger than box
> > > cannot continue, need larger box.
> > >
> > >
> > > Now the rst file show Box dimension: 28.9740000 23.0560000 27.7450000
> > > 90.0000000 90.0000000 90.0000000
> > >
> > >
> > > When I try to run calculation with cut and qmcut value of 8.0, the
> > > calculation even doesn't initiate. So to check if QM is applied to
> proper
> > > residues, I reduced the cut value to 4 (I referred to the mailing list
> > > letters for this). here the calculation begin which eventually ends
> after
> > > some 13000 steps.
> > >
> > > I tried to increase the box size by adding some methanol moelcules ( a
> > box
> > > size around 70 70 70), still the same error appears.
> > >
> > > If the QM is applied to only oneresidue, the calculation runs smoothly,
> > but
> > > not for two residues.
> > > How to work QMMM with QM on 2 residues?
> > >
> > > Please find attached all the needed files which were generated and
> point
> > > out
> > > mistake or suggestions to work out this problem
> > >
> > >
> > > Kaustubh
> > >
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> > >
> >
> >
> > --
> > ================================ Current Address =======================
> > Brian Radak : BioMaPS
> > Institute for Quantitative Biology
> > PhD candidate - York Research Group : Rutgers, The State
> > University of New Jersey
> > University of Minnesota - Twin Cities : Wright-Rieman Hall
> 101
> > Graduate Program in Chemical Physics : 610 Taylor Road,
> > Department of Chemistry : Piscataway, NJ
> > 08854-8066
> > radak004.umn.edu :
> > radakb.biomaps.rutgers.edu
> > ====================================================================
> > Sorry for the multiple e-mail addresses, just use the institute
> appropriate
> > address.
> > _______________________________________________
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> >
> _______________________________________________
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>
--
================================ Current Address =======================
Brian Radak : BioMaPS
Institute for Quantitative Biology
PhD candidate - York Research Group : Rutgers, The State
University of New Jersey
University of Minnesota - Twin Cities : Wright-Rieman Hall 101
Graduate Program in Chemical Physics : 610 Taylor Road,
Department of Chemistry : Piscataway, NJ
08854-8066
radak004.umn.edu :
radakb.biomaps.rutgers.edu
====================================================================
Sorry for the multiple e-mail addresses, just use the institute appropriate
address.
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Received on Thu Oct 06 2011 - 09:00:03 PDT
