From: regafan_at_usc.es
Date: Fri Nov 23 2007 - 12:30:30 CST
Hello,
I am trying to build a DOPC membrane to simulate with NAMD. I have
seen that a pre-equilibrated membrane can be obtained for example from
the webpage of Feller http://persweb.wabash.edu/facstaff/fellers/
In this structure, the residue number is repeating,
ATOM 1 C1 OLEO 1 25.238 -18.360 17.677 0.00 0.00 L001
ATOM 2 O1 OLEO 1 24.822 -17.975 16.590 0.00 0.00 L001
(...)
ATOM 53 N PCGL 2 25.292 -17.626 22.886 0.00 0.00 L001
ATOM 54 C5 PCGL 2 25.325 -18.521 24.083 0.00 0.00 L001
(...)
ATOM 87 C1 OLEO 3 20.132 -19.511 18.765 0.00 0.00 L001
ATOM 88 O1 OLEO 3 20.523 -20.466 18.101 0.00 0.00 L001
(...)
ATOM 140 O1 OLEO 1 -11.817 -26.118 14.598 0.00 0.00 L002
ATOM 141 C2 OLEO 1 -10.529 -25.467 12.598 0.00 0.00 L002
(...)
ATOM 191 N PCGL 2 -14.877 -23.874 19.908 0.00 0.00 L002
ATOM 192 C5 PCGL 2 -14.694 -23.590 18.413 0.00 0.00 L002
(...)
When I try to replicate this system I am having problems. I am using
the following script:
-------------------------------------------------
package require psfgen
topology top_all27_lipid.rtf
mol load pdb dopc_only.pdb
for { set i 0 } { $i <= 2 } { incr i } {
segment LA$i {
auto none
first NONE
last NONE
pdb dopc_only.pdb
}
patch EST1 LA$i:2 LA$i:1
patch EST2 LA$i:2 LA$i:3
coordpdb dopc_only.pdb LA$i
}
for { set i 0 } { $i <= 2 } { incr i } {
segment LB$i {
auto none
first NONE
last NONE
pdb dopc_only.pdb
}
patch EST1 LB$i:2 LB$i:1
patch EST2 LB$i:2 LB$i:3
coordpdb dopc_only.pdb LB$i
}
writepsf bloque_dopc.psf
writepdb bloque_dopc.pdb
mol delete all
mol load psf bloque_dopc.psf pdb bloque_dopc.pdb
for { set i 0 } { $i <= 2 } { incr i } {
set sel1 [atomselect top "segid LA$i"]
set dx [expr 92*$i]
$sel1 moveby "$dx 0 0"
}
for { set i 0 } { $i <= 2 } { incr i } {
set sel1 [atomselect top "segid LB$i"]
set dx [expr 92*$i]
$sel1 moveby "$dx 95 0"
}
# Write everything back out
animate write pdb bicapa_dopc_replicada.pdb
--------------------------------------------------------------
I get the error
ERROR: failed on residue OLEO from pdb file
duplicate residue key 1
ERROR: failed on residue OLEO from pdb file
duplicate residue key 2
ERROR: failed on residue PCGL from pdb file
duplicate residue key 3
ERROR: failed on residue OLEO from pdb file
It is due to the repetition of the residues names along the starting
pdb. I have tried to re-numerate this pdb, but then, I don' t know how
I should to indicate the patch:
patch EST1 LB$i:2 LB$i:1
patch EST2 LB$i:2 LB$i:3
Does anyone knows how to replicate a DOPC membrane for the simulation in NAMD?
Thanks a lot for your help in advance,
Rebeca García Fandiño
Parc Cientific of Barcelona
regafan_at_usc.es
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