From: Law, Yu Kay (lawy_at_iue.edu)
Date: Fri Aug 17 2012 - 23:32:24 CDT

Thanks for the replies!

On Aug 18, 2012, at 0:31, "Suresh" <suresh.gorle_at_research.iiit.ac.in> wrote:

> Hi,
>
> I have never used AutoPSf for generating psf files but i can give an idea about why the problem is appearing. In the top_all36_na.rtf file the patch names DEO1/DEO2 are no longer available and it is renamed to DEOX for non-terminal and DEO5 for 5'-terminal residue. Please check the rtf file.
>
> hope this helps
>
> suresh
>
> ----- Original Message -----
> From: "Yu Kay Law" <lawy_at_iue.edu>
> To: vmd-l_at_ks.uiuc.edu
> Sent: Friday, August 17, 2012 8:50:26 PM
> Subject: vmd-l: CHARMM36 topology files, AutoPSF and DNA
>
> Dear all,
>
> I have tried to use the top_all36_na.rtf file for running AutoPSF using
> VMD 1.9.1 on Mac OS 10.6. The file came from
> http://mackerell.umaryland.edu/download.php?filename=CHARMM_ff_params_files
> /toppar_c36_aug12.tgz and I wanted to use the CHARMM36 edition of the new
> additive DNA force fields.
>
> Unfortunately, when I tried to load this up, the DEO2 patch appears to be
> triggered for no reason and this aborted the setup. I did want the 5TER
> and 3TER patches applied.
>
> The last few lines of the output were as follows:
>
> psfgen) building segment N1
> psfgen) reading residues from pdb file TpA_Bform_autopsf-temp.pdb_N1.pdb
> psfgen) extracted 2 residues from pdb file
> psfgen) setting patch for first residue to 5TER
> psfgen) setting patch for last residue to 3TER
> psfgen) Info: generating structure...psfgen) Info: skipping conformation
> O3'-O5'-P-O2P at beginning of segment.
> psfgen) Info: skipping conformation O3'-O5'-P-O1P at beginning of segment.
> psfgen) Info: skipping conformation O3'-P-O5'-C5' at beginning of segment.
> psfgen) Info: skipping bond O3'-P at end of segment.
> psfgen) Info: skipping conformation C3'-O3'-P-O5' at end of segment.
> psfgen) Info: skipping conformation C4'-C3'-O3'-P at end of segment.
> segment complete.
> psfgen) reading coordinates from pdb file
> TpA_Bform_autopsf-temp.pdb_N1.pdb for segment N1
> psfgen) Warning: failed to set coordinate for atom P T:1 N1
> psfgen) Warning: failed to set coordinate for atom O1P T:1 N1
> psfgen) Warning: failed to set coordinate for atom O2P T:1 N1
> psfgen) applying patch DEO1 to 1 residues
> psfgen) unknown patch type DEO1
>
>
> Could someone please let me know what sort of mistake I've probably made
> here?
>
> Thanks very much.
>
> Yu Kay Law
>
>