Re: [NAMD] Patch 5MC2

From: The Cromicus Productions (thecromicusproductions_at_gmail.com)
Date: Thu Nov 30 2017 - 12:25:55 CST

Never mind, this actually works. The methylated sites are the ones
containing "H5M", not "C5M" as I thought

On Wed, Nov 29, 2017 at 6:45 PM, The Cromicus Productions <
thecromicusproductions_at_gmail.com> wrote:

> 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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