AMBER Archive (2009)

Subject: [AMBER] Inquiries about antechamber

From: Yikan Chen (yc2r_at_virginia.edu)
Date: Wed Aug 26 2009 - 12:07:20 CDT

Hey,
  I have downloaded a pdb file from www.rcsb.org, as shown in the attachment
(1X6W.pdb).
  It cannot be regonized by Amber force fields directly because there is a
TMS residue that is not included in any force field. So I use antechamber to
generate a new pdb file and run it in Gaff. It goes like follows:
  $AMBERHOME/exe/antechamber -i 1X6W_3.pdb -fi pdb -o newff.pdb -fo pdb
  And 1X6W_3.pdb is revised pdb file for antechamber. There are error
messages like the following:

 Unrecognized atomic name JB, exit
 Unrecognized atomic name JB, exit
 Unrecognized atomic name JA, exit
For atom[28]:E2, the best APS is not zero, bonds involved by this atom are
frozen
For atom[29]:GA, the best APS is not zero, bonds involved by this atom are
frozen
For atom[30]:GB, the best APS is not zero, bonds involved by this atom are
frozen
For atom[31]:GC, the best APS is not zero, bonds involved by this atom are
frozen
For atom[32]:A1TT, the best APS is not zero, bonds involved by this atom are
frozen
For atom[33]:B1TT, the best APS is not zero, bonds involved by this atom are
frozen
For atom[38]:E3, the best APS is not zero, bonds involved by this atom are
frozen
For atom[41]:B6, the best APS is not zero, bonds involved by this atom are
frozen
For atom[42]:B7, the best APS is not zero, bonds involved by this atom are
frozen
For atom[46]:JB, the best APS is not zero, bonds involved by this atom are
frozen
For atom[47]:JA, the best APS is not zero, bonds involved by this atom are
frozen
For atom[48]:KA, the best APS is not zero, bonds involved by this atom are
frozen
For atom[49]:KB, the best APS is not zero, bonds involved by this atom are
frozen
For atom[50]:LB, the best APS is not zero, bonds involved by this atom are
frozen
For atom[51]:LA, the best APS is not zero, bonds involved by this atom are
frozen
---Judge bond type for Residue 1 with ID of 1 and Name of S ---
The frozen atom type can only be 1, 2, 3, 7 (aromatic single), 8 (aromatic
double)Error: cannot run
"/itc/apps/amber/10/amber10/bin/bin.Linux.x86_64/bondtype -j full -i
ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac" in
judgebondtype() of antechamber.c properly, exit

 What is that problem? It really puzzles me!
 Thank you very much!

  Best,
  Yikan




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