Hi everybody,
I have obtained docked ligand coordinates from a docking simulation. I added charges and hydrogens to the ligand in Chimera. The PDB file obtained from it looks like what's shown at the end of this message.
Antechamber does not like the connect part giving the message "13 is not a valid atom id in CONECT 13 12 11 10" albeit the fact that the connectivity is correct.
Antechamber accepts the ligand and produces topology files if I remove the CONECT lines. However, it produces the message that there are duplicate C, HC1, HC2 and HC3 atoms. Renaming the atoms following the convention given in the streptavidin tutorial for the biotin molecule (
http://ambermd.org/tutorial/streptavidin/) or indeed any other convention produces warnings like:
Warning: the assigned bond types may be wrong, please :
(1) double check the structure (the connectivity) and/or
(2) adjust atom valence penalty parameters in APS.DAT, and/or
(3) increase PSCUTOFF in define.h and recompile bondtype.c
and the program aborts.
I have two questions:
1. When I remove the CONECT lines and get warnings about duplicate atoms, ARE THESE WARNINGS IMPORTANT or can I live with these?
2. Is there a better method for ligand preparation giving connectivities that Antechamber can understand?
Your help will be greatly appreciated.
George
HETATM 1 C GRA 1 4.146 -4.870 -25.249 1.00 0.00 C
HETATM 2 C GRA 1 4.516 -3.445 -24.944 1.00 0.00 C
HETATM 3 C GRA 1 5.421 -2.751 -25.926 1.00 0.00 C
..........................................................................................................
...........................................................................................................
HETATM 35 HC GRA 1 2.095 -2.703 -32.817 1.00 0.00 H
HETATM 36 O GRA 1 3.772 -2.775 -24.247 1.00 0.00 O
CONECT 13 12 11 10
CONECT 12 13 21 29 30
etc
etc.
...........................................................................................................
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Fri Jan 30 2009 - 01:15:22 PST
