Re: DNA capping

From: Strahs, Dr. Daniel Bernard (
Date: Fri Jun 02 2017 - 07:30:57 CDT

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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