VMD-L Mailing List

From: BIN ZHANG (zhngbn_at_gmail.com)
Date: Wed Dec 09 2009 - 12:07:37 CST

Dear Francesco:

 From the pdb segment you posted, it seems there is one bead missing
in the definition of POPC lipid. Indeed, if you compare the
rbcg-2007.top file posted at : http://www.ks.uiuc.edu/Research/CG/rbcg/files/
  , with the one come with VMD 1.8.7, you will find the difference.

Best,
Bin

On Dec 8, 2009, at 11:23 AM, Francesco Pietra wrote:

> Hi:
> Do restraints on CG models apply like for all-atoms? For example, in
> order to restrain the polar head of POPC lipid
>
> ATOM 2463 CHO POPCO 1 37.490 25.415 4.653 1.00
> 0.00 O1 C
> ATOM 2464 PHO POPCO 1 39.740 24.614 0.940 1.00
> 0.00 O1 P
> ATOM 2465 ES1 POPCO 1 37.568 20.460 -0.263 1.00
> 0.00 O1
> ATOM 2466 ES2 POPCO 1 37.020 21.866 -4.322 1.00
> 0.00 O1
> ATOM 2467 ME1 POPCO 1 36.057 16.858 1.933 1.00
> 0.00 O1
> ATOM 2468 ME2 POPCO 1 35.653 13.060 0.274 1.00
> 0.00 O1
> ATOM 2469 ME3 POPCO 1 37.948 9.854 -0.816 1.00
> 0.00 O1
> ATOM 2470 MT1 POPCO 1 38.047 4.914 0.293 1.00
> 0.00 O1
> ATOM 2471 ME4 POPCO 1 35.557 18.929 -6.037 1.00
> 0.00 O1
> ATOM 2472 ME5 POPCO 1 36.308 15.668 -9.314 1.00
> 0.00 O1
> ATOM 2473 ME6 POPCO 1 37.484 11.986 -12.138 1.00
> 0.00 O1
> ATOM 2474 MT2 POPCO 1 37.279 8.543 -12.520 1.00
> 0.00 O1
> END
>
> are restraints to be applied to beads CHO and PHO? If so, by making
> the .fix file in VMD as if it were an all-atoms model are the
> restraint forces applied correctly?
>
> And if I want to restraint the whole protein and the whole bilayer (to
> work at constant pressure on the solvent water around), is any way to
> simply specify the range of residue numbers?
>
> That is, I assume to have to prepare the system for production as
> carefully as if it were all-atoms.
>
> thanks
> francesco pietra