u should use the topology file and the restart file like:
ambpdb -p file.top < file.crd > file.pdb
do not use the trajectories file
make sure that they are in the same directory
hope it helps
Vijay Manickam Achari wrote:
> Dear amber users..
>
> I have some trouble in creating pdb file with the
> command ambpdb.
> I have runned my simulation and created rst and mdcrd
> files.
> First I used mdcrd file and I tried to generate pdb
> file to see my structure with ambpdb command but it
> state error as below:
>
> [vijay.glycomm03 test1]$ ambpdb -p micelwat.top <
> micelwat_md1_reimage.traj > micelmdcrd.pdb
> | New format PARM file being parsed.
> | Version = 1.000 Date = 05/27/05 Time = 16:04:28
> forrtl: severe (64): input conversion error, unit -5,
> file Internal Formatted Read
> Image PC Routine Line
> Source
> ambpdb 08078309 Unknown
> Unknown Unknown
> ambpdb 08051D89 Unknown
> Unknown Unknown
> ambpdb 08052380 Unknown
> Unknown Unknown
> ambpdb 08062913 Unknown
> Unknown Unknown
> ambpdb 080620A1 Unknown
> Unknown Unknown
> ambpdb 0804DFC0 Unknown
> Unknown Unknown
>
> Stack trace terminated abnormally.
>
> After i getting this kind of message I tried use rst
> file to generate pdb file. But i get the same thing as
> below:
> [vijay.glycomm03 test1]$ ambpdb -p micelwat.top <
> micelwat_md1_rst.traj > micelrst.pdb
> | New format PARM file being parsed.
> | Version = 1.000 Date = 05/27/05 Time = 16:04:28
> forrtl: severe (64): input conversion error, unit -5,
> file Internal Formatted Read
> Image PC Routine Line
> Source
> ambpdb 08078309 Unknown
> Unknown Unknown
> ambpdb 08051D89 Unknown
> Unknown Unknown
> ambpdb 08052380 Unknown
> Unknown Unknown
> ambpdb 08062913 Unknown
> Unknown Unknown
> ambpdb 080620A1 Unknown
> Unknown Unknown
> ambpdb 0804DFC0 Unknown
> Unknown Unknown
>
> Stack trace terminated abnormally.
>
> Can anyone could help me to solve thi problem?
> I badly need your guidance.
>
> Thank you
>
> Vijay
>
>
>
>
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Received on Tue Jun 14 2005 - 12:53:00 PDT
