Re: psfgen error

From: snoze pa (snoze.pa_at_gmail.com)
Date: Wed Feb 03 2010 - 10:25:43 CST

I will suggest, first save the PDB coordinate file in VMD. then use
psfgen from NAMD to create psf and pdb file. Replace last OXT, if any
with OT2, and regular O with OT1.

On Wed, Feb 3, 2010 at 7:35 AM, Anna Dejardin <anna.dejardin_at_ucl.ac.uk> wrote:
> 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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