VMD-L Mailing List

From: JC Gumbart (gumbart_at_ks.uiuc.edu)
Date: Fri Aug 17 2012 - 13:57:45 CDT

The DEO1 patch is (was) needed to convert RNA bases to DNA. However, the header of top_all36_na file explains the problem:

! For DNA update, new atom type required for P of DNA. This required
! replication of a number of parameters and the creation of new
! patches, DEOX and DEO5, to convert RNA to DNA, such that previous
! CHARMM scripts to generate DNA will no longer work. Note that the
! atom type change to P3 ONLY applies to the phosphodester linkage in
! DNA and NOT to terminal phosphates, DMP etc.

This is why I prefer to never use autopsf - it makes many assumptions, some apparent and some hidden. Better to write your own psfgen script (like in the NAMD tutorial), so you know exactly every step involved in building the psf.

On Aug 17, 2012, at 10:20 AM, Law, Yu Kay wrote:

> 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
>