psfgen error

From: Anna Dejardin (anna.dejardin_at_ucl.ac.uk)
Date: Wed Feb 03 2010 - 07:35:54 CST

Hi All,

I am trying to create a .psf file from my .pdb file using psfgen. Some
of the residues in my segment aren't standard but I wrote topology
entries for them and all of the atom names etc match up. However in the
new .pdb file created through psfgen a double bonded carbonyl O on the
end of my segment has been removed and replaced with OT1 and OT2, which
are water oxygens in the topology files. It says it has 'failed to set
coordinate for atom O ', but the coordinates for this atom are given in
the original .pdb. Any ideas why it's not happy? Apologies if this is
really obvious, I'm new to NAMD.
The error messages look like this:

ERROR! FAILED TO RECOGNIZE *>
>>>>>> Includes phi, psi cross term map (CMAP) correction <<<<<<
>>>>>>>>>>>>>>>>>>>>>> July 2004 <<<<<<<<<<<<<<<<<<<<<<<<<<
All comments to ADM jr. via the CHARMM web site: www.charmm.org
parameter set discussion forum

ERROR! FAILED TO RECOGNIZE 31
cross-term entries present in topology definitions
reading topology file top_all35_ethers_mod.inp

ERROR! FAILED TO RECOGNIZE *>>>>>>>>>>>>>>>>>>>
>>>>>>>>>>>>>>>> CHARMM32 ether force field <<<<<<<<<<<<<<<<<<<<<
>>>>>>>>>>>>>>>>>>>>>> December 2006 <<<<<<<<<<<<<<<<<<<<<<<<<<<<
>>>>>>>> Direct comments to Alexander D. MacKerell Jr. <<<<<<<<<<
>>>>>>>>>>>> via the CHARMM forum: www.charmm.org <<<<<<<<<<<<<<<

ERROR! FAILED TO RECOGNIZE 34
duplicate type key HT
duplicate type key OT
duplicate type key HE
duplicate type key NE
duplicate type key DUM
duplicate residue key PROP will be ignored
duplicate residue key TIP3 will be ignored
building segment A
reading residues from pdb file ala_single_noh.pdb
extracted 12 residues from pdb file
Info: generating structure...
Missing atoms for conformation definition
Missing atoms for conformation definition
A:12
Info: segment complete.
reading coordinates from pdb file ala_single_noh.pdb for segment A
Warning: failed to set coordinate for atom O ALAA:12 A
Info: guessing coordinates for 74 atoms (2 non-hydrogen)
Warning: poorly guessed coordinates for 41 atoms (2 non-hydrogen):
Warning: poorly guessed coordinate for atom H1A DEC:1 A
Warning: poorly guessed coordinate for atom H1C DEC:1 A
Warning: poorly guessed coordinate for atom HS DEC:1 A
Warning: poorly guessed coordinate for atom H3A DEC:1 A
Warning: poorly guessed coordinate for atom H3B DEC:1 A
Warning: poorly guessed coordinate for atom H4A DEC:1 A
Warning: poorly guessed coordinate for atom H4B DEC:1 A
Warning: poorly guessed coordinate for atom H5A DEC:1 A
Warning: poorly guessed coordinate for atom H5B DEC:1 A
Warning: poorly guessed coordinate for atom H6A DEC:1 A
Warning: poorly guessed coordinate for atom H6B DEC:1 A
Warning: poorly guessed coordinate for atom H7A DEC:1 A
Warning: poorly guessed coordinate for atom H7B DEC:1 A
Warning: poorly guessed coordinate for atom H8A DEC:1 A
Warning: poorly guessed coordinate for atom H8B DEC:1 A
Warning: poorly guessed coordinate for atom H9A DEC:1 A
Warning: poorly guessed coordinate for atom H9B DEC:1 A
Warning: poorly guessed coordinate for atom H10A DEC:1 A
Warning: poorly guessed coordinate for atom H10C DEC:1 A
Warning: poorly guessed coordinate for atom H2A PEGM:2 A
Warning: poorly guessed coordinate for atom H2B PEGM:2 A
Warning: poorly guessed coordinate for atom H1B PEGM:3 A
Warning: poorly guessed coordinate for atom H1A PEGM:3 A
Warning: poorly guessed coordinate for atom H2A PEGM:3 A
Warning: poorly guessed coordinate for atom H2B PEGM:3 A
Warning: poorly guessed coordinate for atom H1B PEGM:4 A
Warning: poorly guessed coordinate for atom H1A PEGM:4 A
Warning: poorly guessed coordinate for atom H2A PEGM:4 A
Warning: poorly guessed coordinate for atom H2B PEGM:4 A
Warning: poorly guessed coordinate for atom H1B PEGM:5 A
Warning: poorly guessed coordinate for atom H1A PEGM:5 A
Warning: poorly guessed coordinate for atom H2A PEGM:5 A
Warning: poorly guessed coordinate for atom H2B PEGM:5 A
Warning: poorly guessed coordinate for atom HT1 AMA:6 A
Warning: poorly guessed coordinate for atom HN1 LYSA:9 A
Warning: poorly guessed coordinate for atom HN2 LYSA:9 A
Warning: poorly guessed coordinate for atom HA ALA:11 A
Warning: poorly guessed coordinate for atom OT1 ALAA:12 A
Warning: poorly guessed coordinate for atom OT2 ALAA:12 A
Warning: poorly guessed coordinate for atom HA ALAA:12 A
Warning: poorly guessed coordinate for atom HO ALAA:12 A
Warning: failed to guess coordinates for 7 atoms

Thanks for any help.

Anna

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