[NAMD] Patch 5MC2

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

This archive was generated by hypermail 2.1.6 : Mon Dec 31 2018 - 23:20:43 CST