VMD-L Mailing List

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Sun Jan 03 2010 - 09:24:22 CST

Please disregard the thread. I have finally solved (it prevented me to
modify/add chains, finally, I have to think back how I managed, it
allowed0
f.

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Sun, Jan 3, 2010 at 11:54 AM
Subject: vmd-l: Failure of AutoSCFBuilder to recognize all monomers
To: vmd <vmd-l_at_ks.uiuc.edu>

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