Re: DNA capping

From: Nicholus Bhattacharjee (nicholusbhattacharjee_at_gmail.com)
Date: Fri Jun 02 2017 - 09:57:41 CDT

Hello Lennart,

With top_all27_prot_na.inp topology I used following patches to get 5TER,
3TER and deoxy, and it works fine

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%
segment ADNA {

     first 5TER
     last 3TER

     pdb ADNA.pdb
}

puts "Begin to patch to make DEOXYribose"

  # patch to make DEOXYribose
  # purine use patch DEO2
  # pyrimidine use patch DEO1

foreach segid $segidList tmpList $patchList {
puts "segid: $segid tmpList:$tmpList"
     foreach record $tmpList {
        foreach {resid resname} $record { break }
        if {$resname == "THY" || $resname == "CYT" } {
            patch DEO1 ${segid}:$resid
            puts "patch DEO1 ${segid}:$resid"
        }

        if {$resname == "ADE" || $resname == "GUA" } {
            puts "patch DEO2 ${segid}:$resid"
            patch DEO2 ${segid}:$resid
        }
     }
     coordpdb ${segid}.pdb

}

%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%

If now I use top_all36_na.rtf topology and change DEO1 & DEO2 to DEOX it
works but gives an extra atom (P in index 0). Can you kindly let me know
how should I use patch with top_all36_na.rtf. Thank you in advance.

On Fri, Jun 2, 2017 at 4:10 PM, Lennart Nilsson <Lennart.Nilsson_at_ki.se>
wrote:

> With c36 the deoxy paching scheme has changed and does not depend on the
> base anymore, but there is a separate patch for the 5' residue.
>
>
>
>
>
>
>
> Best wishes,
> Lennart Nilsson
>
>
>
> *From:* owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] *On
> Behalf Of *Nicholus Bhattacharjee
> *Sent:* den 2 juni 2017 14:38
> *To:* Strahs, Dr. Daniel Bernard <dstrahs_at_pace.edu>
> *Cc:* namd-l_at_ks.uiuc.edu
>
> *Subject:* Re: namd-l: DNA capping
>
>
>
> Hello Dan,
>
> Thank you. Actually I could find a psfgen input file to cap as well as
> make the residues deoxy. It is working fine with top_all27_prot_na.inp
> topology file but if I use top_all36_na.rtf topology file it is showing
> error due to absence of patch DEO1 and DEO2. So do I use patch from
> top_all27_prot_na.inp for this purpose. Thank you again.
>
>
>
> On Fri, Jun 2, 2017 at 2:30 PM, Strahs, Dr. Daniel Bernard <
> dstrahs_at_pace.edu> wrote:
>
> We would need more information on your psfgen input.
>
>
>
> This is a working example from my research:
>
>
>
> segment S {
> pdb NoEnhancement2.pdb
> first none
> last none
> }
> patch 5TER S:1
> patch DEO1 S:1
> patch DEO2 S:2
> patch DEO1 S:3
> patch DEO1 S:4
> patch DEO2 S:5
> patch DEO1 S:6
> patch DEO1 S:7
> patch DEO2 S:8
> patch DEO1 S:9
> patch DEO1 S:10
> patch DEO1 S:11
> patch DEO1 S:12
> patch 3TER S:12
> coordpdb NoEnhancement2.pdb S
>
>
>
> Dan Strahs
>
>
> ------------------------------
>
> *From:* owner-namd-l_at_ks.uiuc.edu <owner-namd-l_at_ks.uiuc.edu> on behalf of
> Nicholus Bhattacharjee <nicholusbhattacharjee_at_gmail.com>
> *Sent:* Friday, June 2, 2017 8:09 AM
> *To:* namd-l_at_ks.uiuc.edu
> *Subject:* Re: namd-l: DNA capping
>
>
>
> Hello all,
>
> After some searching in google I found the following command to cap DNA.
>
> $ segment A {first 5TER last 3TER pdb init.pdb}
>
> However it is giving me the following error
>
> psfgen) building segment A
> argument: presname
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> ERROR: failed while building segment
>
> Can someone kindly help on this.
>
> Thanks
>
>
>
> On Thu, Jun 1, 2017 at 11:11 AM, Nicholus Bhattacharjee <
> nicholusbhattacharjee_at_gmail.com> wrote:
>
> Hello all,
>
> I would like to know how to cap DNA strand with 5' and 3' with the help of
> psfgen. Working with the commands of psfgen it seems like for me unlike
> proteins/peptides DNA is not capped automatically. Can someone help me with
> this. Moreover, is it necessary to cap DNA strands in 5' and 3' termini.
> Thank you in advance for the answer.
>
> Regards
>
>
>
>
>

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