Re: symmetric behavior

From: Narender Singh Maan (nsmaan_at_gmail.com)
Date: Thu Aug 13 2009 - 14:17:43 CDT

Thanxs Joshua. Offhand i don't have these articles but I am sure i have read
such article (i will search them out sometime soon and will post them)...
meanwhile i am having another problem with psfgen....(a related post is
already on mailing list....
( http://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l/4923.html )
.........
I have obtained a preequilibrated POPC membrane (264 total) from another
source which doesn't contain hydrogens. Now i am using psfgen to make them
but some generated hydrogen bond lengts are very unrealistic, when viewed in
vmd with psf
My popc.pdb is like this...
..........................
ATOM 1 N POPCL 1 -39.724 -9.327 23.120 1.00 0.00 POPC
ATOM 2 C11 POPCL 1 -39.508 -10.519 23.971 1.00 0.00 POPC
ATOM 3 C12 POPCL 1 -41.144 -9.249 22.551 1.00 0.00 POPC
ATOM 4 C13 POPCL 1 -41.200 -9.167 23.647 1.00 0.00 POPC
ATOM 5 C14 POPCL 1 -40.999 -10.083 22.911 1.00 0.00 POPC
ATOM 6 C15 POPCL 1 -39.380 -11.827 24.690 1.00 0.00 POPC
ATOM 7 P1 POPCL 1 -41.828 -13.028 24.891 1.00 0.00 POPC
ATOM 8 O3 POPCL 1 -41.228 -13.025 23.526 1.00 0.00 POPC
....
and psfgen.pgn is
....
package require psfgen
topology top_all27_prot_lipid.rtf
segment POPC {
  pdb popc.pdb
  first NONE
  last NONE
  }
coordpdb popc.pdb POPC
guesscoord
regenerate angles dihedrals
writepsf xl.psf
writepdb xl.pdb
..............................
Any help please...

Thank you
NS

On Wed, Aug 12, 2009 at 10:49 AM, Joshua Adelman <jadelman_at_berkeley.edu>wrote:

> WIthout knowing anything about the specific system you are talking about, I
> would say the "similarity" between the subunits depends on several things,
> foremost among them, how you define "similarity". The second issue you might
> consider, is if this homopentamer is quite large (and even if it isn't) then
> you could run into a timescale issue. Depending on how you defined your
> metric of similarity, even if on average the subunits should all behave in
> the same way, correlation times longer than the time of the simulation might
> make them appear to behave differently.
>
> Could you post some information (Authors,Year,Journal) for the articles
> that you were referring to?
>
> Josh
>
>
>
> On Aug 12, 2009, at 7:16 AM, Narender Singh Maan wrote:
>
> Hello, Just wanted to know other users experience and opinion on this:
>> In a 'totally' symmetric homopentameric structure, shouldn't all the
>> subunits behave in a similar fashion during simulation?. I have seen
>> articles both ways; in which such symmetric subunits behave in a similar or
>> dissimilar fashion.....any thoughts...
>> Thank you
>> NS
>>
>
>

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