Re: DNA capping

From: Strahs, Dr. Daniel Bernard (
Date: Fri Jun 02 2017 - 10:01:52 CDT

Use DEO5 for the 5' residue, then DEOX for the remaining residues, and then try applying 5TER.

Sorry; haven't built ssDNA in c36 yet.

Dan Strahs

From: Nicholus Bhattacharjee <>
Sent: Friday, June 2, 2017 10:57 AM
To: Lennart Nilsson
Cc:; Strahs, Dr. Daniel Bernard
Subject: Re: namd-l: DNA capping

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 <<>> 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:<> [<>] On Behalf Of Nicholus Bhattacharjee
Sent: den 2 juni 2017 14:38
To: Strahs, Dr. Daniel Bernard <<>>

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 <<>> 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:<> <<>> on behalf of Nicholus Bhattacharjee <<>>
Sent: Friday, June 2, 2017 8:09 AM
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.

On Thu, Jun 1, 2017 at 11:11 AM, Nicholus Bhattacharjee <<>> 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.

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