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

From: The Cromicus Productions (thecromicusproductions_at_gmail.com)
Date: Fri Jun 09 2017 - 12:31:08 CDT

Hi everyone, sorry to come back to this but there's something I haven't
been able to solve and that is
how to work with the boundary conditions of the box. I would guess in order
to simulate the periodic DNA
the first and last nucleotides must be very close and we shouldn't have any
water in the middle. Also, the distances
involved should be the same than for a regular pair of base pairs. How can
this be solved? Do I just consider
a slightly smaller box than my DNA and hope for the best during
minimization?

Thanks!

Sebastian

On Sun, May 7, 2017 at 1:03 AM, The Cromicus Productions <
thecromicusproductions_at_gmail.com> wrote:

> 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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