Re: problems replicating a DOPC membrane

From: Richard Swenson (swenson_at_hec.utah.edu)
Date: Thu Nov 29 2007 - 14:57:35 CST

Rebeca,

I'm sure there are quicker ways to build a DOPC membrane than mine, but
here's how I do it:

1) I used `grep segid original_file.pdb>segid` to store each segment in
a separate pdb file (I don't include the .pdb extension do denote that
the numbering is off). I also combined all of fellers lipid segments
into one larger segment by catting the pdb files and then using find and
replace to change all of the segids to the same identifier.

2) I then used the bash script (reformat.sh) that uses awk to renumber
each segment. From the command line type ./reformat.sh segid for each
segment file. This will renumber segid and create segid.pdb which
should be a correctly formatted pdb file.

3) I then used the attached tcl scripts to make pdb and psf files for
each segment. From the command line type vmd -dispdev text dopc_psf.tcl.

4) The final system was created by using the system_psf.tcl script as in
step3.

I prefer the modular approach because it is easier for me to debug and
modify the structure to make big membranes. Don't forget to change the
directories in each script to match yours. Good luck.

Richard

regafan_at_usc.es wrote:
>
> 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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