SanDisk Membrain Software Manual de usuario descargar pdf (Pagina 28)

2 PLACING KCSA IN A MEMBRANE 28

3 Use VMD to look at the selections created and try to ﬁnd a better selection

criteria so as to keep as much non-overlapping lipids as possible around

KcsA.

4 As we saw above, the membrane also came with some water molecules

solvating its headgroups. We must remove the water molecules overlapping

with the protein:

set seltext4 "(water and not segname WCA WCB WCC WCD WF SOLV) \

and same residue as within 3 of \

((same residue as (name P1 and beta>0)) or protein)"

set seltext5 "segname SOLV and same residue as \

within 3 of lipids"

set sel4 [atomselect top $seltext4]

set sel5 [atomselect top $seltext5]

$sel4 set beta 1

$sel5 set beta 1

set badwater [atomselect top "name OH2 and beta > 0"]

set seglistwater [$badwater get segid]

set reslistwater [$badwater get resid]

5 Now, we delete the atoms as we did before:

mol delete all

resetpsf

readpsf kcsa popc raw.psf

coordpdb kcsa popc raw.pdb

foreach segid $seglistlipid resid $reslistlipid {

delatom $segid $resid

}

foreach segid $seglistwater resid $reslistwater {

delatom $segid $resid

}

writepsf kcsa popc.psf

writepdb kcsa popc.pdb

6 Load the ﬁles kcsa popc.psf and kcsa popc.pdb into VMD and check

that there is no overlap between the channel and the membrane (Fig. 8).

As usual, if you detect something wrong, you may want to regenerate the

ﬁles using the script remove lipwat.tcl

We are almost there! We only have to solvate (with VMD this time) and ionize

the system, then we can start using NAMD to actually perform a simulation of

KcsA in its native-like environment.

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SanDisk Membrain Software Manual de usuario Pagina 28