VMD-L Mailing List

From: SYEDA SABIHA SULTANA LUBNA . (p20190061_at_hyderabad.bits-pilani.ac.in)
Date: Thu Aug 19 2021 - 06:34:02 CDT

Hi,
Can someone please explain to me this script for developing a mutated model
in VMD.

"package require psfgen

proc mutate_res {pos mut prot} {
# in pdb file $prot.pdb, mutate the residue at position $pos to a
# residue of type $mut
#set pos 2
#set mut TRP
#set prot tnc

set file_in $prot.pdb
set file_tmp $prot.temp.pdb
set file_out_pdb $prot.mut.pdb
set file_out_psf $prot.mut.psf

set str "all and not (resid $pos and sidechain)"
mol new tnc.pdb type pdb
set sel [atomselect top $str]
$sel writepdb $file_tmp

resetpsf
package require psfgen
topology top_all27_prot_lipid.inp
pdbalias residue HIS HSE
pdbalias atom ILE CD1 CD
segment P {
  pdb $file_tmp
  mutate $pos $mut}
  coordpdb $file_tmp P
  guesscoord
  writepdb $file_out_pdb
  writepsf $file_out_psf
  mol delete top
  mol new $file_out_pdb type pdb
}" 

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