VMD-L Mailing List
From: David E. Heppner (heppner_at_alumni.stanford.edu)
Date: Wed May 04 2016 - 05:02:00 CDT
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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 guesscoord 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 exit ---------------------------------------------- David E. Heppner, Ph.D. david.heppner_at_med.uvm.edu heppner_at_alumni.stanford.edu > On May 3, 2016, at 5:29 PM, Josh Vermaas <vermaas2_at_illinois.edu> 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 >> david.heppner_at_med.uvm.edu <mailto:david.heppner_at_med.uvm.edu> >> heppner_at_alumni.stanford.edu <mailto:heppner_at_alumni.stanford.edu> >> Department of Pathology and Laboratory Medicine >> Department of Chemistry >> University of Vermont >
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