VMD-L Mailing List

From: Prof. Eddie (eackad_at_siue.edu)
Date: Tue Mar 09 2021 - 13:00:06 CST

Hi all,
I am still following this
<https://www.ks.uiuc.edu/Research/namd/mailing_list/namd-l.2017-2018/0432.html>
thread
to perform the psfgen on the console so I can insert a mutate command.
However, as I run the script and generate the pdb and psf I get atoms
defined in charmm36m but then some of the basic dihedrals are missing when
I check with fftk. To test it I just run it without any mutate. I still get
dihedrals that are missing parameters such as
NH3 CT1 CT2 HA2
NH3 CT1 CT2 CT2
HC NH3 CT1 HB1

but no missing bonds or angles. I've tried using just the prm files as well
as all the prm and str files but fftk still says that I am missing those
dihedrals.

I've added the aliasing from psfgen and the complete script is below. Any
ideas on my mistake?
Thanks!

#Log the procedure
set outname "orig"
psfgen_logfile "psfgen_${outname}.log"
package require psfgen
resetpsf
topology ../toppar_c36_jul20/top_all36_cgenff.rtf
topology ../toppar_c36_jul20/top_all36_carb.rtf
topology ../toppar_c36_jul20/top_all36_lipid.rtf
topology ../toppar_c36_jul20/top_all36_prot.rtf
topology ../toppar_c36_jul20/top_interface.rtf
topology ../toppar_c36_jul20/stream/prot/toppar_all36_prot_heme.str
topology ../toppar_c36_jul20/toppar_water_ions.str

##### the following was taken from
http://www.ks.uiuc.edu/Research/vmd/plugins/autopsf/tech.html
 pdbalias residue G GUA
  pdbalias residue C CYT
  pdbalias residue A ADE
  pdbalias residue T THY
  pdbalias residue U URA

  foreach bp { GUA CYT ADE THY URA } {
     pdbalias atom $bp "O5\*" O5'
     pdbalias atom $bp "C5\*" C5'
     pdbalias atom $bp "O4\*" O4'
     pdbalias atom $bp "C4\*" C4'
     pdbalias atom $bp "C3\*" C3'
     pdbalias atom $bp "O3\*" O3'
     pdbalias atom $bp "C2\*" C2'
     pdbalias atom $bp "O2\*" O2'
     pdbalias atom $bp "C1\*" C1'
  }

  pdbalias atom ILE CD1 CD
  pdbalias atom SER HG HG1
  pdbalias residue HIS HSD

# Heme aliases
  pdbalias residue HEM HEME
  pdbalias atom HEME "N A" NA
  pdbalias atom HEME "N B" NB
  pdbalias atom HEME "N C" NC
  pdbalias atom HEME "N D" ND

# Water aliases
  pdbalias residue HOH TIP3
  pdbalias atom TIP3 O OH2

# Ion aliases
  pdbalias residue K POT
  pdbalias atom K K POT
  pdbalias residue ICL CLA
  pdbalias atom ICL CL CLA
  pdbalias residue INA SOD
  pdbalias atom INA NA SOD
  pdbalias residue CA CAL
  pdbalias atom CA CA CAL

# Other aliases
  pdbalias atom LYS 1HZ HZ1
  pdbalias atom LYS 2HZ HZ2
  pdbalias atom LYS 3HZ HZ3

  pdbalias atom ARG 1HH1 HH11
  pdbalias atom ARG 2HH1 HH12
  pdbalias atom ARG 1HH2 HH21
  pdbalias atom ARG 2HH2 HH22

  pdbalias atom ASN 1HD2 HD21
  pdbalias atom ASN 2HD2 HD22

segment P1 {
    pdb apo_protein.pdb
    first NTER
    last CTER
}
coordpdb apo_protein.pdb P1

guesscoord

writepdb "p450_prot_apo_${outname}.pdb"
writepsf "p450_prot_apo_${outname}.psf"
psfgen_logfile close 

-- 
_________________________________________________________
Edward Ackad, Ph.D <https://urldefense.com/v3/__http://www.siue.edu/*7Eeackad__;JQ!!DZ3fjg!tkwHziiIbryQxSGXDlohYJGT3Vmzs_cjljXcnn9psgG_j_GNquESPtqVtTKjBVx6fA$ >
Associate Professor of Physics
Computational Nanophotonics
Southern Illinois University Edwardsville
(618) 650-2390