Need help preventing hydration of the lipid-protein interface in my system

From: Maggie Pruitt (mamdahl_at_iastate.edu)
Date: Fri Nov 19 2010 - 09:46:45 CST

Hello,

I am interested in modeling the G protein-coupled receptor I study. I have built the protein in a POPE lipid bilayer and solvated it with water and counter ions. I have modeled my simulations after the “Membrane Proteins Tutorial" and am at the point where I want to minimize and equilibrate the system with only the protein constrained.

When I do this, water molecules move into the hydrophobic part of the membrane. The tutorial uses the Tcl script named keep_water_out.tcl to prevent this hydration of the membrane-protein interface. I would like to modify this script for my protein, but am unsure where to begin. I have looked into the “User-defined Forces in NAMD” tutorial but I am still stuck, being I am not familiar with Tcl scripts.

The specific section of the Tcl script that I believe I need to modify is under the “user definitions” section, where it lists a number of water molecules after “set watexcept.” How can I know which water molecules in my system need to be defined here?

Below is an excerpt of the Tcl script.

Thanks in advance for your help!

Maggie

#!/usr/local/bin/namd2
# keep water from entering gaps between protein and lipids
# need membrane be in the XY plane!
# (C) A. Aksimentiev (alek_at_ks.uiuc.edu)

# This script will prevent water molecules in your namd simulations
# from entering into the hydrophobic part of the membrane. This can be very
# useful for initial equilibration of a protein/lipid/water system.
# It works with recent NAMD binaries (version 2.4 and higher), which
# has clearconfig command.

# Brief description:
# At initialization, the arrays of namd atom indices of all water oxygens
# and of all lipid c21 carbons are created. They will be used later to
# determine which water molecules to push out of the membrane and to compute
# membrane dimensions. At every simulation step the pushing forces are applied
# to a minor number of atoms, which doesn't affect NAMD performance. The
# membrane dimensions are recalculated every N steps (regulated by the global
# parameter $lipidCheckFreq) as well as the indices of the
# water molecules that will be pushed during the next N steps (regulated by
# the global parameter $waterCheckFreq). The membrane should be in XY plane.
# To use this script one has to add the following lines to the namd
# configuration script (without "#" symbol):
#
#
# set waterCheckFreq 100
# set lipidCheckFreq 100
# set allatompdb a1b2c5_init.pdb
# tclForces on
# tclForcesScript keep_water_out.tcl
#
# # lipidCheckFreq must be an integer multiple of waterCheckFreq .

###################################################################
# user definitions begin
###################################################################

print "Starting Tcl forces"

# define force constant per group (Kcal/(mol*A))
set fconst 0.1
set pressure 1.0
set fconstUp [expr $fconst*$pressure]
set fconstDown [expr -$fconst*$pressure]

# define water and lipid names
set watResName "TIP3"
set watAtomName "OH2"
set lipResName "POPC"
set lipAtomName "C1 "

# define exceptions

set watexcept {30621 30624 30627 30630 30633 30642 30648 30654 30669 30678 30687 30690 30711 30717 30720 30744 30747 30756 30759 30762 30768 30801 30807 30816 30828 30843 30846 30852 30864 30888 30906 30927 30933 30936 30957 30960 30972 32546 32549 32552 32555 32558 32567 32579 32594 32603 32612 32615 32636 32642 32645 32669 32672 32681 32684 32687 32693 32726 32732 32741 32753 32768 32771 32777 32789 32813 32831 32852 32858 32861 32882 32885 32897 34471 34474 34477 34480 34483 34492 34498 34504 34519 34528 34537 34540 34561 34567 34570 34594 34597 34606 34609 34612 34618 34651 34657 34666 34678 34684 34693 34696 34702 34714 34738 34756 34777 34783 34786 34798 34807 34810 34822 36396 36399 36402 36405 36408 36417 36429 36444 36453 36462 36465 36486 36492 36495 36519 36522 36531 36534 36537 36543 36576 36582 36591 36603 36618 36621 36627 36639 36663 36681 36702 36708 36711 36732 36735 36747 36754 36757 36760}

###################################################################
# user definitions stop here!
###################################################################

This archive was generated by hypermail 2.1.6 : Wed Feb 29 2012 - 05:23:24 CST