VMD-L Mailing List

From: Suresh (suresh.gorle_at_research.iiit.ac.in)
Date: Fri Aug 17 2012 - 23:30:41 CDT

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