From: The Cromicus Productions (thecromicusproductions_at_gmail.com)
Date: Sat May 06 2017 - 23:30:26 CDT
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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