From: Roshan Shrestha (roshanpra_at_gmail.com)
Date: Thu Jul 06 2017 - 17:53:51 CDT
Thanks Josh, but I am getting this error while using this script as it is.
The error is:
*psfgen) Info: generating structure...psfgen) unknown residue type
DCfailed!ERROR: failed on end of segmentMOLECULE DESTROYED BY FATAL ERROR!
Use resetpsf to start over*
On Thu, Jul 6, 2017 at 11:18 PM, Vermaas, Joshua <Joshua.Vermaas_at_nrel.gov>
wrote:
> Hi Roshan,
>
> If you have VMD 1.9.3, the automatic psf builder in VMD is super easy.
> Just load your pdb, then click the buttons in the appropriate order (top to
> bottom). It guesses the waters correctly and picks up that it is meant to
> be DNA automatically. If you only care about this particular pdb, this is
> the easiest way to do it. However, that is no fun, so here is how I'd do it
> manually, since to me, "manually" means writing a script for it, which
> makes it much more flexible if you want to do something strange in the
> future. These scripts to make psfs are pretty generic, and always do three
> things: load a topology file, create a segment, and assign atomic positions
> to atoms in the segment. There is a slight wrinkle if you are doing this
> manually, since the default it to have the all nucleic acids be RNA, and
> you want DNA. This can be handled in the script pretty easily. The full
> script for VMD is below, and only assumes you've downloaded the pdb and the
> appropriate topology for DNA.
>
> -Josh
>
> package require psfgen
> resetpsf
> topology top_all36_na.rtf
> mol new 1bna.pdb
> set chaina [atomselect top "chain A and not water"]
> $chaina writepdb A.pdb
> set chainb [atomselect top "chain B and not water"]
> $chainb writepdb B.pdb
> segment DA {
> pdb A.pdb
> first 5TER
> last 3TER
> }
> #Make this DNA, not RNA
> patch DEO5 DA:1
> for { set i 2 } { $i <= [llength [lsort -unique [$chaina get resid]]]} {
> incr i } {
> patch DEOX DA:$i
> }
> segment DB {
> pdb B.pdb
> first 5TER
> last 3TER
> }
> #For comparison, we are leaving chain B unpatched, which leaves it as
> RNA!!!
>
> #Load in coordinates
> coordpdb A.pdb DA
> coordpdb B.pdb DB
>
> regenerate angles dihedrals
> guesscoord
>
> writepsf dna.psf
> writepdb dna.pdb
>
> #inspect your handiwork
> mol load psf dna.psf pdb dna.pdb
>
> On 07/06/2017 10:54 AM, Roshan Shrestha wrote:
> I am trying to create psf for 1bna.pdb (DNA) using CHARMM36 force field
> either manually or using automatic psf builder in VMD. But, I am lost on
> how shall I start or do it. I would be very grateful if anyone could
> suggest me the steps to start with. Thanks
>
> --
> Roshan Shrestha
> Graduate Student
> Central Department of Physics,Tribhuvan University
> Kathmandu,Nepal
>
>
>
>
>
-- Roshan Shrestha Graduate Student Central Department of Physics,Tribhuvan University Kathmandu,Nepal
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