VMD-L Mailing List

From: Maxim Belkin (mbelkin_at_ks.uiuc.edu)
Date: Sat Aug 16 2014 - 03:33:34 CDT

Right. AutoPSF is "tuned" for CHARMM27 that had that DEO1 patch. Now (in CHARMM36) it's DEOX non 5-terminal nucleotides and DEO5 for 5-terminal ones.

DEO1 and DEO2 patches are hard-coded into AutoPSF for dna, so to change this you would have to modify its source code.

I suggest you to look into psfgen and its user guide.

Maxim

On Aug 16, 2014, at 3:08 AM, Ashar Malik <asharjm_at_gmail.com> wrote:

> Thanks for the reply Maxim, I am sure you are refering to the GUI where I can set it to read a different topology file by selecting a location with the new topology file.
>
> That works with Proteins but with Nucleic acids there is a problem. I can not generate the psf with "top_all36_na"
>
> The error is:
>
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> while executing
> "patch DEO1 $segname:$resid"
>
> DEO1 is the patch name from the top_all27_prot_na file. The program is expecting this patch, but in top_all36_na this has been renamed DEO5 i think.
>
> I can do a manual change to this but I don't want to get anything wrong.
>
> A few questions:
>
> How does the program still expect DEO1 when that information is not in the Topology file I provided?
>
> Where is this information stored so I can change it as well instead of manually making changes to the program (manually setting location of the topology file in the PSF dialog -- If i delete the old files and replace them with new ones will they automatically be loaded) ?
>
> With the Automatic PSF builder I have to set the path everytime, can this be avoided? Does this read *.str files that can be used to read multiple topologies (protein + nucleic acids) in one go?
>
> Best,
>
>
> On Sat, Aug 16, 2014 at 7:13 PM, Maxim Belkin <mbelkin_at_ks.uiuc.edu> wrote:
> Ashar, you can do what you want in "Step 1" section of AutoPSF plugin window (Extension -> Modeling -> Automatic PSF builder).
>
> Maxim
>
> On Aug 15, 2014, at 9:23 PM, Ashar Malik <asharjm_at_gmail.com> wrote:
>
> > Hi,
> >
> > I work with VMD 1.9.1 and want to know how to change the topology files that VMD uses when I am using the AutoPSF generate plugin.
> >
> > I want to update those files to match the latest files available with the most recent CHARMM36 release.
> >
> > VMD 1.9.1
> >
> > VMD\plugins\noarch\tcl\readcharmmpar1.2
> >
> > currently holds an old release of the files.
> >
> > I want to add the new topology files here and parameters files to readcharmmpar1.2 so that i can work with the most optimized values.
> >
> > --
> > Best,
> > /A
>
>
>
>
> --
> Best,
> /A