Re: DNA capping

From: Nicholus Bhattacharjee (
Date: Fri Jun 02 2017 - 07:09:08 CDT

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.
> Regards

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