I tried autoimage first as it is suggested in manual, but it did not
worked. Only after that I tried unwrap & image combination
On Jun 22, 2017 5:57 PM, "Daniel Roe" <daniel.r.roe.gmail.com> wrote:
> What happens if you just 'autoimage' (don't unwrap first)?
>
> -Dan
>
> On Thu, Jun 22, 2017 at 9:51 AM, SHAILESH KUMAR <shaile27_sit.jnu.ac.in>
> wrote:
> > Dear Fellows,
> >
> > I have performed a MD simulation with coordinates wrapping enabled. Now I
> > am facing discontinuous trajectory problem. I tried to unwrap coordinates
> > and reimage but it did not helped. Investigating about the cause of
> problem
> > I found following things.
> >
> > 1. PBC Box dimensions: {88.588371 75.344688 67.300514 90.000000 90.000000
> > 90.000000}
> > 2. Protein dimension (distance between coordinates of extreme points in
> > protein) as
> > {63.625731468200684 49.82566452026367 40.63145446777344}
> >
> > Unwrapping and Imaging was done as below with cpptraj.
> >
> > parm com.wat.leap.prmtop
> > trajin rst2_out.dcd 1 51000 10
> > reference ../../../../02.leap/com/com.wat.leap.inpcrd
> > unwrap byres reference !:1-287
> > center :123.HE2 mass origin reference
> > image origin center familiar com :123.HE2 byres !:1-287
> > unwrap byatom reference :1-287
> > center :123.HE2 mass origin reference
> > image origin center familiar com :123.HE2 byatom :1-287
> > trajout com.strip_cr14.nc
> > go
> >
> > Atom :123.HE2 was nearest protein atom to the center of PBC box in
> initial
> > coordinates, hence it was chosen for centering protein to the box.
> >
> > Now, problem is that molecule has rotated during the simulation in the
> box
> > and hence atoms are crossing two opposite sides of the box at the same
> > time. So, when it is wrapped these atoms are appearing from opposite of
> > actual side it should be, leading to stretches of structure connected by
> > bonds length of box-dimension.
> >
> > So, I tried to construct a cubic box of side length 20 with is center at
> > the center of PBC-box.
> > as follows.
> >
> > Let centre of PBC-box has coordinates {cx cy cz}
> > then six-set of residues corresponding to residues beyond inner-cubic-box
> > faces were selected as
> >
> > set rset1 [atomselect top "protein and x < cx - 10"]
> > set rset1 [atomselect top "protein and x > cx + 10"]
> > set rset1 [atomselect top "protein and y < cy - 10"]
> > set rset1 [atomselect top "protein and y > cy + 10"]
> > set rset1 [atomselect top "protein and z < cz - 10"]
> > set rset1 [atomselect top "protein and z > cz + 10"]
> >
> > Now residues in these sets were unwraped
> > centering was done with atom closet to the center of corresponding face
> of
> > inner-cubic-box
> > and image was done for these set of residues. but it dis not work
> >
> > Other suggested options were also tried e.g.
> >
> > unwrap
> > autoimage
> >
> > with bymol, byres and byatom options with solute mask, all system mask,
> but
> > yet to succeed.
> >
> > Any help and suggestions in regard will be greatly appreciated.
> >
> > Thank you.
> >
> > Image of system with/without box waters shown is attached. If required, I
> > can share, prmtop and dcd files with some frames.
> >
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
>
> --
> -------------------------
> Daniel R. Roe
> Laboratory of Computational Biology
> National Institutes of Health, NHLBI
> 5635 Fishers Ln, Rm T900
> Rockville MD, 20852
> https://www.lobos.nih.gov/lcb
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Jun 22 2017 - 10:00:02 PDT
