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
> >
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Received on Tue Dec 12 2017 - 08:30:02 PST
