From: David E. Heppner (
Date: Wed May 04 2016 - 05:02:00 CDT

Thank you for the reply. I coped the script below if that helps.

mol load pdb 2src.pdb
set proa [atomselect top protein]   
$proa writepdb proa.pdb
package require psfgen
pdbalias residue HIS HSE 
pdbalias atom ILE CD1 CD
pdbalias residue PTR TYR
topology toppar/top_all36_prot.rtf
topology toppar/top_all36_na.rtf
topology toppar/toppar_all36_prot_fluoro_alkanes.str
topology toppar/toppar_all36_prot_na_combined.str
topology toppar/toppar_water_ions_namd.str
segment PROA {
    pdb proa.pdb
    mutate 239 HSD 
    mutate 492 HSD    
patch TP2 PROA:527
regenerate angles dihedrals
coordpdb proa.pdb PROA
writepdb prot.pdb
writepsf prot.psf
package require solvate
solvate prot.psf prot.pdb -x 0 -y 0 -z 0 +x 20 +y 20 +z 20 -o solv_box
package require autoionize
autoionize -psf solv_box.psf -pdb solv_box.pdb -sc 0.15 -cation POT  # salt concentration
animate delete all
David E. Heppner, Ph.D.
> On May 3, 2016, at 5:29 PM, Josh Vermaas <> wrote:
> Hi Dave,
> Did you guess coordinates? If psfgen doesn't know where the atom is, and you don't let it guess after regenerating angles and dihedrals, it will place everything at the origin.
> -Josh
> On 05/03/2016 03:29 PM, David E. Heppner wrote:
>> Dear All,
>> I’m encountering a problem when trying to patch a phosphotyrosine residue with VMD. It seems to be a common problem, as seen in other posts, where the structure that is generated in NAMD has all three terminal oxygen of the phosphate at the same x,y,z coordinates. However, I cannot seem to correct this problem.
>> The solution to this, as recommended, is to include “autogenerate angles dihedrals” or “regenerate angles dihedrals” after the patch command. For example,
>> patch TP2 PROA:180
>> regenerate angles dihedrals
>> Even if this is included, NAMD gives a structure where the oxygen atoms are at the same x,y,z, coordinates. Please let me know if you have any suggestions of how to properly deal with this issue. 
>> Best,
>> 	Dave Heppner
>> ----------------------------------------------
>> David E. Heppner
>> <>
>> <>
>> Department of Pathology and Laboratory Medicine
>> Department of Chemistry
>> University of Vermont