Re: [NAMD] How to build and simulate a periodic DNA in NAMD

From: The Cromicus Productions (thecromicusproductions_at_gmail.com)
Date: Sun May 07 2017 - 00:03:43 CDT

I found the problem, it's not the same to add res 1 70 than 70 1 hehe

On Sun, May 7, 2017 at 12:30 AM, The Cromicus Productions <
thecromicusproductions_at_gmail.com> wrote:

> Sorry to bother again, I'm currently running into a problem of the kind
> "UNABLE TO FIND ANGLE PARAMETERS FOR..." the atoms that I have
> just bonded. Have you ran into that problem before?
>
> On Sat, May 6, 2017 at 8:02 PM, The Cromicus Productions <
> thecromicusproductions_at_gmail.com> wrote:
>
>> Thank you very much, Steve! I used the patch "LKNA" instead of "PBCrna"
>> and I think it worked great!
>>
>> On Sat, May 6, 2017 at 2:49 PM, Nielsen, Steven <
>> steven.nielsen_at_utdallas.edu> wrote:
>>
>>> Hi Sebastian,
>>>
>>> Adding a "patch" to your topology file is the easiest way.
>>> In my case, which is for the helical RNA strand in the TMV virus,
>>> I wanted to make the RNA strand infinitely long.
>>> My "pgn" file looks like:
>>> ---------------------------------
>>> package require psfgen
>>> topology top_all27_prot_na_SON.inp
>>> # add RNA
>>> segment RNA {first none; last none; pdb rna.pdb}
>>> coordpdb rna.pdb RNA
>>> patch PBCrna RNA:1 RNA:150
>>> guesscoord
>>> regenerate angles dihedrals
>>> guesscoord
>>> writepdb x.pdb
>>> writepsf x.psf
>>> -----------------------------------
>>>
>>> The key here is the patch command. My "PBCrna" patch, in the topology
>>> file, looks like:
>>> -------------
>>> PRES PBCrna 0.0
>>> BOND 1P 2O3'
>>> --------------
>>>
>>> That's it!! The "regenerate" command generates the correct bends and
>>> dihedrals to
>>> accompany the bond that I added. This patch adds a bond between atom
>>> "1P" on the
>>> first RNA base and the atom "2O3'" on the last (#150) RNA base.
>>>
>>> Note: in VMD the bond will be drawn across the box, but that is just how
>>> VMD displays
>>> it, it really it across the PBC.
>>>
>>> -Steve
>>>
>>>
>>> ________________________________________
>>> From: owner-namd-l_at_ks.uiuc.edu [owner-namd-l_at_ks.uiuc.edu] on behalf of
>>> The Cromicus Productions [thecromicusproductions_at_gmail.com]
>>> Sent: Saturday, May 6, 2017 1:14 PM
>>> To: NAMD list
>>> Subject: namd-l: [NAMD] How to build and simulate a periodic DNA in NAMD
>>>
>>> Hi everyone,
>>>
>>> I'd like to simulate an infinitely long, periodic dsDNA in NAMD.
>>> To do so I read in Nano Lett., 2015, 15 (12), pp 8322–8330 that I must
>>> covalently bond the ends of the DNA to their periodic copies.
>>> Any idea of which would be the easiest way to do this?
>>>
>>> Thank you very much,
>>>
>>> Sebastian
>>>
>>
>>
>

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