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
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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 Tue Dec 12 2017 - 06:00:05 PST
