Fwd: vmd-l: Restraints on coarse grained model

From: Francesco Pietra (chiendarret_at_gmail.com)
Date: Wed Dec 09 2009 - 03:07:36 CST

I went on with the VMD TkConsole commands

$all set beta 0

set fixed [atomselect top "protein or (chain O and name CHO PHO)"]

$fixed set beta 1

It worked for the lipid, not for the protein, whose beta column
(tempFactor in PDB language) 0.00 was unchanged.

I found no way out from manuals. Do cg proteins behave differently
from all-atoms proteins to these commands or I just made some mistake?
Should a Python script be prepared to modify the beta column for the
protein?

thanks
francesco

---------- Forwarded message ----------
From: Francesco Pietra <chiendarret_at_gmail.com>
Date: Tue, Dec 8, 2009 at 8:23 PM
Subject: vmd-l: Restraints on coarse grained model
To: vmd <vmd-l_at_ks.uiuc.edu>

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

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