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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Received on Tue Dec 12 2017 - 04:30:05 PST
