AMBER Archive (2006)

Subject: RE: AMBER: Combining Residues in LEaP for Lipid Bilayers

From: Matthew Tessier (matthew.tessier_at_gmail.com)
Date: Mon Nov 20 2006 - 11:48:32 CST

Here are my input commands, the prep file names are also the residue names:

source /home/matt/parameterization/1004leaprc.Glycam_04
loadamberparams /home/matt/parameterization/Glycam_04_lipids.dat
 

# Head group
loadamberprep 1PC.prep
 

# Middle group (connects head and tail)
loadamberprep 3GY.prep
 

# Tail groups (SN1 and SN2)
loadamberprep MYR.prep
loadamberprep MY2.prep
 

#Connecting the prep files
set 1PC tail 1PC.1.O1
set 3GY head 3GY.1.C1
linear = sequence { 1PC 3GY }
set linear tail linear.2.O2
set MYR head MYR.1.C1
linear = sequence { linear MYR }
set linear tail linear.2.O1
set MY2 head MY2.1.C1
lipid1 = sequence { linear MY2 }
desc lipid1

#Assigning the correct geometeries
impose MY2 {1} { {C3 C4 C5 C6 -90} }
impose MYR {1} { {C1 C2 C3 C4 160} }

#Aligning the lipid along the z-axis with a template pdb
impose lipid1 {3} { {C13 C14 C15 C16 0.0} }
lipid1 = loadpdb POPC2.pdb
transform lipid1 { { 1 0 0} { 0 0 1} { 0 1 0} }
 

charge lipid1

#Combining the different residue units into one name
DMP = combine { 1PC 3GY MYR MY2 }

# Row 1 - includes lipid1
lipid2 = copy lipid1
translate lipid2 { 5.1 2.5 0 }
 

lipid3 = copy lipid2
translate lipid3 { 5.1 -2.5 0 }
 

lipid4 = copy lipid3
translate lipid4 { 5.1 2.5 0 }
 

lipid5 = copy lipid4
translate lipid5 { 5.1 -2.5 0 }
 

lipid6 = copy lipid5
translate lipid6 { 5.1 2.5 0 }
 

# Row 2
lipid7 = copy lipid1
translate lipid7 { 0 9.8 0 }
 

lipid8 = copy lipid7
translate lipid8 { 5.1 2.5 0 }
 

lipid9 = copy lipid8
translate lipid9 { 5.1 -2.5 0 }
 

lipid10 = copy lipid9
translate lipid10 { 5.1 2.5 0 }
 

lipid11 = copy lipid10
translate lipid11 { 5.1 -2.5 0 }
 

lipid12 = copy lipid11
translate lipid12 { 5.1 2.5 0 }
 

# Row 3
lipid13 = copy lipid7
translate lipid13 { 0 9.8 0 }
 

lipid14 = copy lipid13
translate lipid14 { 5.1 2.5 0 }
 

lipid15 = copy lipid14
translate lipid15 { 5.1 -2.5 0 }
 

lipid16 = copy lipid15
translate lipid16 { 5.1 2.5 0 }
 

lipid17 = copy lipid16
translate lipid17 { 5.1 -2.5 0 }
 

lipid18 = copy lipid17
translate lipid18 { 5.1 2.5 0 }

# Row 4
lipid19 = copy lipid13
translate lipid19 { 0 9.8 0 }
 

lipid20 = copy lipid19
translate lipid20 { 5.1 2.5 0 }
 

lipid21 = copy lipid20
translate lipid21 { 5.1 -2.5 0 }
 

lipid22 = copy lipid21
translate lipid22 { 5.1 2.5 0 }
 

lipid23 = copy lipid22
translate lipid23 { 5.1 -2.5 0 }
 

lipid24 = copy lipid23
translate lipid24 { 5.1 2.5 0 }
 

# Row 5
lipid25 = copy lipid19
translate lipid25 { 0 9.8 0 }
 

lipid26 = copy lipid25
translate lipid26 { 5.1 2.5 0 }
 

lipid27 = copy lipid26
translate lipid27 { 5.1 -2.5 0 }
 

lipid28 = copy lipid27
translate lipid28 { 5.1 2.5 0 }
 

lipid29 = copy lipid28
translate lipid29 { 5.1 -2.5 0 }
 

lipid30 = copy lipid29
translate lipid30 { 5.1 2.5 0 }
 

# Row 6
lipid31 = copy lipid25
translate lipid31 { 0 9.8 0 }
 

lipid32 = copy lipid31
translate lipid32 { 5.1 2.5 0 }
 

lipid33 = copy lipid32
translate lipid33 { 5.1 -2.5 0 }
 

lipid34 = copy lipid33
translate lipid34 { 5.1 2.5 0 }
 

lipid35 = copy lipid34
translate lipid35 { 5.1 -2.5 0 }
 

lipid36 = copy lipid35
translate lipid36 { 5.1 2.5 0 }

# Building the monolayer
upper = combine { lipid1 lipid2 lipid3 lipid4 lipid5 lipid6 lipid7 lipid8
lipid9 lipid10 lipid11 lipid12 lipid13 lipid14 lipid15 lipid16 lipid17
lipid18 lipid19 lipid20 lipid21 lipid22 lipid23 lipid24 lipid25 lipid26
lipid27 lipid28 lipid29 lipid30 lipid31 lipid32 lipid33 lipid34 lipid35
lipid36 }
 

# Building the bilayer (reflecting the monolayer)
lower = copy upper
transform lower { { -1 0 0 } { 0 -1 0 } { 0 0 -1 } }
translate lower { -35 -3 1 }
dmpc_all = combine { upper lower }

#setBox dmpc_all vdw 0
solvateBox dmpc_all TP3 { 0 0 11 } 1.6

savepdb dmpc_all DMPC_bilayerWAT.pdb
saveamberparm dmpc_all DMPC_bilayerWAT.top DMPC_bilayerWAT.crd

-----Original Message-----
From: owner-amber_at_scripps.edu [mailto:owner-amber_at_scripps.edu] On Behalf Of
David A. Case
Sent: Monday, November 20, 2006 12:35 PM
To: amber_at_scripps.edu
Subject: Re: AMBER: Combining Residues in LEaP for Lipid Bilayers

On Mon, Nov 20, 2006, Matthew Tessier wrote:

> I start
> off with 4 units for each of the groups (the DMPC tail groups are the same
> but have different unit names) and attach them together using the head
and
> tail commands. Each of these four units has a corresponding residue name.
> Once the units are combined together, they still retain their original
> residue names.

Can you post the commands you actually used?

...thx...dac

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