AMBER Archive (2005)

Subject: AMBER: creating pdb file....

From: Vijay Manickam Achari (vjrajamany_at_yahoo.com)
Date: Tue Jun 14 2005 - 05:49:09 CDT

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_at_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_at_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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