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
Received on Tue Dec 12 2017 - 05:30:09 PST
