From: Nicholus Bhattacharjee (nicholusbhattacharjee_at_gmail.com)
Date: Fri Jun 02 2017 - 07:38:24 CDT
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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