AMBER Archive (2004)

Subject: AMBER: question about mm_pbsa and nmode

From: Xiao He (hx_at_itcc.nju.edu.cn)
Date: Mon Oct 11 2004 - 02:43:53 CDT

Dear Amber users,

  One Amber group's JACS paper said that, residues for molecular dynamic simulations, PBSA, and
normal mode calculations for HIV-1 RT/TIBO and efavirenz. All the
residues in cyan and red as well as the ligand are flexible during the
molecular dynamics simulations; all the residues in red (without water)
including the ligand are used for normal mode calculations; all the
residues in magenta and the flexible residues of receptor as well as the
ligand (without water) are applied for PBSA calculations.

  The normal mode calculation is extremely time-consuming for large
systems; thus, only residues within 12 Å of the mass center of the
ligand (including the ligand, but excluding water molecules) were used
for the normal mode calculation (red and interior area in Figure 3).

  How to restrain the unmoved residues in mm_pbsa input to do pbsa and nmode calculaion?

Thanks a lot!

He Xiao

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