Hi Andrea,
I did a search on google and found the guideline for how does a model
file should end to be readable in XPLOR:
"Finally, the file should end with 1) the C-terminal oxygen, 2) an
extra oxygen atom labeled "OT", at coordinates slightly different from
the previous oxygen, and 3) the line "END", as in the following
example for PDB format:
ATOM 20852 C PHE 5373 252.950 402.164 482.294 1.00136.36
ATOM 20853 O PHE 5373 252.000 401.978 483.069 1.00136.95
ATOM 20854 OT PHE 5373 251.990 401.968 483.079 1.00136.95
END
source : http://bilbo.bio.purdue.edu/~baker/high_to_low/EditXPLOR.html
You may possibly try the tips. However, I am not sure if the
conventions have been changed in the current version, that probably
you will be using.
-Pooja
On 11 Feb 2009, at 23:53, Andrea Berry wrote:
Hello,
I have a homology model that I would like to use as my starting PDB
for simulated annealing. However, I am having trouble generating PSF
and PDB files from the starting PDB file. The starting PDB file does
not have any side chain protons. The last atom on the starting PDB
file is:
ATOM 1092 OXT VAL 181 21.394 9.485 -2.085 1.00 0.00
when I use a generate.inp script, I get
%ATMCHK-ERR: unknown coordinates for atom " -181 -VAL -OT1 :"
9999.000 9999.000 9999.000
%ATMCHK-ERR: unknown coordinates for atom " -181 -VAL -OT2 :"
9999.000 9999.000 9999.000
%ATMCHK-ERR: Unknown coordinates
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
BOMLEV= 0 reached. Program execution will be terminated.
%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
Subroutine DIE called . Terminating
So.... I deleted the OXT line to see if generate.inp would pick OT1
and OT2 values for me, but the same error occured.
Then... I replaced the OXT line with two lines labeled OT1 and OT2
(tried it two ways, with coordinates of 0, 0, 0, and coordinates
that were in the ballpark of my other coordinates).
This gave me the error I'm most confused about: Earlier in the
output file, I see the following:
COOR>!EXPDTA MODEL, MODELLER Version 6v2 2004/10/04 14:27:21.443
COOR>ATOM 1 N ASN 37 -21.045 -1.061 -4.921 1.00
0.00
COOR>ATOM 2 CA ASN 37 -20.826 -0.456 -6.252 1.00
0.00
%COOR-ERR: ERROR during reading coordinates
%COOR-ERR: unrecognized command:
ATOM
^^^^
CREAD: reading a harvard coordinate file
%COOR-ERR: ERROR during reading coordinates
%COOR-ERR: unrecognized command:
ATOM 1091 OT1
^^^
%COOR-ERR: unrecognized command:
ATOM 1091 OT1 VAL
And the error ^^^ symbols continue to advance word by word through
the next several lines. So, to me it looks like it sees the word
"ATOM" of atoms of 1091 and 1092 as an error, even though the lines
for atoms 1091 and 1092 are formatted exactly the same as all the
other lines above. It's true that I inserted these lines and made up
OT1 and OT2 values, but the error begins even before those made up
values are read.
I looked very carefully to make sure that I used O and zero
correctly on these lines. I also did everything in vi, so I don't
think there are any incompatibilites with a text editor. All of the
pdb files that I am trying to use as input (the one with OX1, the
one with no terminal O, and the one with invented OT1 and OT2) are
readable by a pdb reader (Pymol), and identical overlying structures
are seen.
Does anyone have any thoughts on what I'm doing wrong, or other
approaches to making psf and pdb files from an incomplete pdb file?
I hope that all made sense, and I really appreciate any thoughts or
comments.
Thank you,
Andrea
****************************************************
Andrea A. Berry, M.D.
Fellow, Pediatric Infectious Diseases
University of Maryland School of Medicine
Center for Vaccine Development
[email protected]
phone 410-706-5328
pager 410-748-0003
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