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 > aberry at medicine.umaryland.edu > phone 410-706-5328 > pager 410-748-0003 > > > > Confidentiality Statement: > This email message, including any attachments, is for the sole use > of the intended recipient(s) and may contain confidential and > privileged information. Any unauthorized use, disclosure or > distribution is prohibited. If you are not the intended recipient, > please contact the sender by reply email and destroy all copies of > the original message. > _______________________________________________ > Xplor-nih mailing list > Xplor-nih at nmr.cit.nih.gov > http://dcb.cit.nih.gov/mailman/listinfo/xplor-nih -------------- next part -------------- An HTML attachment was scrubbed... URL: http://dcb.cit.nih.gov/pipermail/xplor-nih/attachments/20090216/99ed78a3/attachment.html
