Can you describe exactly how the intial 'autoimage' did not work? Your
best bet for getting help is to provide your exact input and as
precise a description of the original problem as possible.
-Dan
On Thu, Jun 22, 2017 at 12:47 PM, SHAILESH KUMAR <shaile27_sit.jnu.ac.in> wrote:
> 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
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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
> _______________________________________________
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> 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
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Received on Thu Jun 22 2017 - 13:00:03 PDT
