Oh I see, then the large number could be diffusion. Did you visualize like
Dan said?
On Dec 12, 2017 11:07 AM, "Myron" <myron.qmandmd.gmail.com> wrote:
> I have tried autoimage. However, I use implicit solvent so there is no box
> information.
> Amber complained that
>
> ACTION SETUP FOR PARM '../mys.top' (2 actions):
>
> 0: [autoimage]
>
> Warning: autoimage: Parm ../mys.top does not contain box information.
>
> Warning: Setup failed for [autoimage]: Skipping
>
> On Tue, Dec 12, 2017 at 7:23 AM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
> > Try using image (or autoimage) in your script.
> >
> > On Dec 12, 2017 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
> > >
> > _______________________________________________
> > 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
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Tue Dec 12 2017 - 10:00:02 PST
