generate question

Balaji Bhyravbhatla balaji at sb.fsu.edu
Thu Apr 9 14:13:30 EST 1998


Dear All,
I would appreciate if someone could point out what I am doing wrong in
generating a psf file.
I a testing it out with a truncated version of the pdb file which I will
include also. The problem is that I am getting this error:

%SEGMNT-ERR: segid in coordinate file does not match 

in XPLOR. I have tried to use the inp file for the tutorial etc. but I
am obviously doing something wrong. Here is the input file:

*********************************************************************
topology  @TOPPAR:tophcsdx.pro  end                             
parameter  @TOPPAR:parhcsdx.pro   end

segment   
  name="AAAA"
  chain
    @TOPPAR:toph19.pep 
  {===>} coordinates @a.pdb 
  end                          
end   
coordinates @a.pdb 
stop
 vector do (name="O") ( name OT1 )               {*names are
used.         *}
***********************************************************************

Here is the pdb file:

ATOM      1  N   LEU     4      39.700  74.869  -1.062  1.00 19.27     
AAAA
ATOM      2  CA  LEU     4      39.677  73.478  -0.636  1.00 19.27     
AAAA
ATOM      3  CB  LEU     4      38.440  73.208   0.218  1.00  8.61     
AAAA
ATOM      4  CG  LEU     4      38.315  73.718   1.666  1.00  8.61     
AAAA
ATOM      5  CD1 LEU     4      38.689  75.162   1.832  1.00  8.61     
AAAA
ATOM      6  CD2 LEU     4      36.857  73.577   1.991  1.00  8.61     
AAAA
ATOM      7  C   LEU     4      39.680  72.521  -1.860  1.00 19.27     
AAAA
ATOM      8  O   LEU     4      39.502  71.304  -1.721  1.00  8.61     
AAAA
ATOM      9  N   VAL     5      39.938  73.059  -3.041  1.00  7.82     
AAAA
ATOM     10  CA  VAL     5      39.965  72.254  -4.231  1.00  7.82     
AAAA
ATOM     11  CB  VAL     5      41.088  71.187  -4.171  1.00 23.72     
AAAA
ATOM     12  CG1 VAL     5      41.089  70.359  -5.427  1.00 23.72     
AAAA
ATOM     13  CG2 VAL     5      42.415  71.879  -3.938  1.00 23.72     
AAAA
ATOM     14  C   VAL     5      38.627  71.535  -4.384  1.00  7.82     
AAAA
ATOM     15  O   VAL     5      38.032  71.571  -5.448  1.00 23.72     
AAAA
ATOM     16  N   ASP     6      38.163  70.902  -3.316  1.00  5.00     
AAAA
ATOM     17  CA  ASP     6      36.865  70.247  -3.274  1.00  5.00     
AAAA
ATOM     18  CB  ASP     6      36.906  68.785  -3.715  1.00 25.55     
AAAA
ATOM     19  CG  ASP     6      35.529  68.168  -3.795  1.00 25.55     
AAAA
ATOM     20  OD1 ASP     6      35.285  67.362  -4.722  1.00 25.55     
AAAA
ATOM     21  OD2 ASP     6      34.657  68.534  -2.997  1.00 25.55     
AAAA
ATOM     22  C   ASP     6      36.312  70.347  -1.837  1.00  5.00     
AAAA
ATOM     23  OT1 ASP     6      36.837  69.762  -0.917  1.00 25.55     
AAAA
ATOM     23  OT2 ASP     6      36.837  69.762  -0.917  1.00 25.55     
AAAA
END   


****************************************************************************

PLease reply if you can see the problem.


Thanks to all.

Balaji
-- 
Florida State University                           
Institute of Molecular Biophysics                   
Room 412 -- (904) 644 6547                       
balaji at sb.fsu.edu



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