From: The Cromicus Productions (thecromicusproductions_at_gmail.com)
Date: Wed Nov 29 2017 - 17:45:16 CST
Hi everyone,
I'm having problems with patch 5MC2 for methylation of DNA bases.
I want to methylate only the 5th base from chain A, so I write
set all [atomselect top all]
set sel [atomselect top "all and chain A and name C1'"]
set seg DNAA
segment $seg {
first 5TER
last 3TER
pdb dsdna_A.pdb
}
patch 5MC2 $seg:5
However, when I look at the code, all the bases have been methylated. Any
clue of what could I be doing incorrectly?
Thanks a lot!
Sebastian
P.S.: My total code is:
mol load pdb dsdna.pdb
set all [atomselect top all]
$all moveby [vecinvert [measure center $all weight mass]]
$all moveby "0 0 20"
set A [atomselect top "all and chain A"]
set B [atomselect top "all and chain B"]
$all writepdb dsdna.pdb
$A writepdb dsdna_A.pdb
$B writepdb dsdna_B.pdb
package require psfgen
resetpsf
topology ff/top_all36_na.rtf
topology ff/toppar_all36_na_modifications.str
mol load pdb dsdna.pdb
set all [atomselect top all]
set sel [atomselect top "all and chain A and name C1'"]
set seg DNAA
segment $seg {
first 5TER
last 3TER
pdb dsdna_A.pdb
}
#this part methylates resid 5
patch 5MC2 $seg:5
foreach resid [$sel get resid] resname [$sel get resname] {
if { $resid eq "1"} {
patch DEO5 $seg:$resid
} else {
patch DEOX $seg:$resid
}
}
coordpdb dsdna_A.pdb $seg
set sel [atomselect top "all and chain B and name C1'"]
set seg DNAB
segment $seg {
first 5TER
last 3TER
pdb dsdna_B.pdb
}
foreach resid [$sel get resid] resname [$sel get resname] {
if { $resid eq "1"} {
patch DEOX $seg:$resid
} else {
patch DEOX $seg:$resid
}
}
coordpdb dsdna_B.pdb $seg
guesscoord
regenerate angles dihedrals
writepsf dsdna2a.psf
writepdb dsdna2a.pdb
mol load pdb dsdna2a.pdb psf dsdna2a.psf
set badwater [atomselect top "all and chain B and name P and resid 1"]
set seglist [$badwater get segid]
set reslist [$badwater get resid]
foreach segid $seglist resid $reslist {
delatom $segid $resid P
}
guesscoord
regenerate angles dihedrals
guesscoord
regenerate angles dihedrals
guesscoord
writepsf dsdna2.psf
writepdb dsdna2.pdb
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