VMD-L Mailing List
From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sun Jan 03 2010 - 04:54:24 CST
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Hi:
The issue is that for a sbcg file made of (although I was unable with
gmail to get real
plain text, column alignment is perfect, as shown in the attachment)
ATOM 1 A1 HAS X 1 56.429 53.644 18.701 1.00 1.00 P1
........................
ATOM 44 A44 HAS X 1 52.923 92.219 35.075 1.00 44.00 P1
ATOM 1 A1 HAS X 1 102.381 56.694 31.262 1.00 1.00 P1
.........................
ATOM 44 A44 HAS X 1 82.135 88.319 11.685 1.00 44.00 P1
ATOM 1 A1 HAS X 1 68.854 62.941 65.469 1.00 1.00 P1
...........................
ATOM 44 A44 HAS X 1 86.145 95.542 49.060 1.00 44.00 P1
ATOM 1 PCH DOPCX 1 117.769 29.749 0.813 1.00 0.00 P
...........................
ATOM 194 DOT DOPCX 128 33.187 6.948 84.855 1.00 0.00 D
END
Well, AutoPSF (vmd 1.8.7 linux64) only works for the third monomer in
the above list,
and the lipid. I mean that the pdf generated along with the psf file
only contains the third
monomer.
The three monomers are identical, so that I used a single .top file
(generated while making the three cg models for the three monomers of
this homotrimer)
for all them. Of course also a .top file for the lipid.
On the other hand, in these various attempts, with the same monomer
.top file, it also occurred
that only the first one of the above monomers was dealt with.
Therefore the problem
should not be with the .top file.
Before posting for help, I have long managed with the above input pdb
by making the
chain ID (here X for all) different for the different monomers. Or
changing the last column
(here P1 at col 73 74 for all monomers). At no avail.
I am not using the script provided by the sbcg tutorial to combine
monomers and membrane
because i am at a very different model. I used my methods to combine
the pieces (which
worked fine for the same system with rbcg).
Thanks for help
francesco pietra
- text/plain attachment: attachment.txt
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