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
aberry at medicine.umaryland.edu
phone 410-706-5328
pager 410-748-0003
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