Yeah, I agree which puzzles me a lot because basically I uses the same
setting as previous simulation I have done.
So this time I tried to simulate a long Myosin protein which is long I
agree but the value looks too large.
(1) Amber version : Amber 14 and AmberTools are alongside the verion.
(2) I use mdcrd output coordinate sets saved over trajectory so the
outputfile trajectory is like mys001.coord , mys002.coord
(3) I tried VMD but nothing can be show from my trajectory which made me
realize that the trajectory contains too large values too.
I can only visualize the first 2 frames and from Frame 3, the value becomes
too large to be shown in VMD.
Best,
On Tue, Dec 12, 2017 at 7:52 AM, Daniel Roe <daniel.r.roe.gmail.com> wrote:
> Hi,
>
> Those coordinates are insanely large. That combined with the fact that
> there are no significant digits after the decimal point indicates to
> me that something is strange.
>
> 1) What version of Amber/AmberTools are you using?
> 2) What format are your input trajectories in (ASCII/NetCDF)?
> 3) Are you able to visualize your input trajectories (e.g. with VMD)?
>
> -Dan
>
> On Tue, Dec 12, 2017 at 7:26 AM, Myron <myron.qmandmd.gmail.com> wrote:
> > I am using Amber to simulate a long protein link. Although the simulation
> > goes well, but the simulation result looks every puzzling. I tried to use
> > Amber to generate a series of PDB files but the generated PDB file looks
> > like this:
> >
> > ATOM 6 HA LYS 1
> > -234821288583424.000-610838750948.00023925014113984.000 1.00 0.00
> > H
> > ATOM 7 CB LYS 1
> > -234821288583424.000-610838750948.00023925014113984.000 1.00 0.00
> > C
> > ATOM 8 HB2 LYS 1
> > -234821288583424.000-610838750948.00023925014113984.000 1.00 0.00
> > H
> > ATOM 9 HB3 LYS 1
> > -234821288583424.000-610838750948.00023925014113984.000 1.00 0.00
> > H
> > ATOM 10 CG LYS 1
> > -234821288583424.000-610838750948.00023925014113984.000 1.00 0.00
> > C
> > ATOM 11 HG2 LYS 1
> > -234821288583424.000-610838750948.00023925014113984.000 1.00 0.00
> > H
> > ATOM 12 HG3 LYS 1
> > -234821288583424.000-610838750948.00023925014113984.000 1.00 0.00
> > H
> > ATOM 13 CD LYS 1
> > -234821288583424.000-610838750948.00023925014113984.000 1.00 0.00
> > C
> > ATOM 14 HD2 LYS 1
> > -234821288583424.000-610838750948.00023925014113984.000 1.00 0.00
> > H
> > ATOM 15 HD3 LYS 1
> > -234821288583424.000-610838750948.00023925014113984.000 1.00 0.00
> > H
> >
> > So I think this is due the drifting of protein, so I try to add the*
> center
> > origin *command in CPPtraj but the problem remains.
> >
> > I am very confused why this error happens.
> > And here is my CPPtraj scripts:
> >
> > parm ../mys.top
> > trajin ../mys001.coord 1 50000 10
> > #trajin ../mys002.coord 1 50000 100
> > #trajin ../mys003.coord 1 50000 100
> > #trajin ../mys004.coord 1 50000 1000
> >
> > center origin
> >
> > trajout tmp.nc
> > trajout pdb/mdp.pdb pdb multi
> >
> >
> > It would be great if you can tell me where I use the wrong options in the
> > CPPtraj scripts.
> >
> > Best,
> > Myron
> > _______________________________________________
> > 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
>
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Received on Tue Dec 12 2017 - 08:30:03 PST
