From: The Cromicus Productions (thecromicusproductions_at_gmail.com)
Date: Sat May 06 2017 - 19:02:57 CDT
Thank you very much, Steve! I used the patch "LKNA" instead of "PBCrna" and
I think it worked great!
On Sat, May 6, 2017 at 2:49 PM, Nielsen, Steven <steven.nielsen_at_utdallas.edu
> wrote:
> Hi Sebastian,
>
> Adding a "patch" to your topology file is the easiest way.
> In my case, which is for the helical RNA strand in the TMV virus,
> I wanted to make the RNA strand infinitely long.
> My "pgn" file looks like:
> ---------------------------------
> package require psfgen
> topology top_all27_prot_na_SON.inp
> # add RNA
> segment RNA {first none; last none; pdb rna.pdb}
> coordpdb rna.pdb RNA
> patch PBCrna RNA:1 RNA:150
> guesscoord
> regenerate angles dihedrals
> guesscoord
> writepdb x.pdb
> writepsf x.psf
> -----------------------------------
>
> The key here is the patch command. My "PBCrna" patch, in the topology
> file, looks like:
> -------------
> PRES PBCrna 0.0
> BOND 1P 2O3'
> --------------
>
> That's it!! The "regenerate" command generates the correct bends and
> dihedrals to
> accompany the bond that I added. This patch adds a bond between atom "1P"
> on the
> first RNA base and the atom "2O3'" on the last (#150) RNA base.
>
> Note: in VMD the bond will be drawn across the box, but that is just how
> VMD displays
> it, it really it across the PBC.
>
> -Steve
>
>
> ________________________________________
> From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of
> The Cromicus Productions [thecromicusproductions_at_gmail.com]
> Sent: Saturday, May 6, 2017 1:14 PM
> To: NAMD list
> Subject: namd-l: [NAMD] How to build and simulate a periodic DNA in NAMD
>
> Hi everyone,
>
> I'd like to simulate an infinitely long, periodic dsDNA in NAMD.
> To do so I read in Nano Lett., 2015, 15 (12), pp 8322–8330 that I must
> covalently bond the ends of the DNA to their periodic copies.
> Any idea of which would be the easiest way to do this?
>
> Thank you very much,
>
> Sebastian
>
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