RE: protein interact with its image

From: Blake Charlebois (bdc_at_mie.utoronto.ca)
Date: Tue Apr 19 2005 - 12:10:20 CDT

Hi Shunzhou,

There is precedent (Gao, Craig, Vogel, Schulten, J. Mol. Biol. 323:939,
2002) for harmonically restraining the protein termini. However, this was a
study of a fibronectin repeat, which, in vivo, would not have termini, but
would be covalently bound at both ends to another fibronectin repeat (I
believe). Therefore, it could be argued that these restraints are somewhat
realistic. You would not be able to make this argument for just any protein.

NAMD allows harmonic restraints (see the constraints section of the manual)
to be applied in only one, only two, or all three of the Cartesian axis
directions.

Blake

-----Original Message-----
From: owner-namd-l_at_ks.uiuc.edu [mailto:owner-namd-l_at_ks.uiuc.edu] On Behalf
Of Shunzhou Wan
Sent: April 19, 2005 11:24 AM
To: namd-l_at_ks.uiuc.edu
Subject: namd-l: protein interact with its image

Hi,

I am running a NPT simulation with PBC. The protein rotates during a
long simulation (25ns). The longest axis of protein deviates from the
longest axis of the box. The other two dimensions are not long enough
when the longest axis of protein is in these direction (protein is too
close to its image in one dimension). It is very computational expensive
to use a cubic box.

Would there be a way of suppressing the rotation of protein, or resizing
the waterbox? Any help/suggestions would be appreciated. Thanks!

Shunzhou//

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