From: White, Mark (mawhite_at_UTMB.EDU)
Date: Thu Oct 29 2020 - 18:10:37 CDT


I found a strange difference in behaviour between the VMD packages PSFGEN and AUTOPSF.

I can use AUTOPSF to generate a TIP3 solvated and SOD/CLA ionized PDB/PSF file. However, it does not apply the CYSD patch by deleting the CYS HG1 atom, but by setting the atom positions to {0,0,0}.

If I use PSFGEN then it does not use the CHARM26 atom types HB1 and HA2, but HB and HA. It appears to use the top_all27_prot_lipid_na.inp TOPPOLOGY file even though the CHARMM26 files are specified and recognized

I am running the following script in VMD:

package require psfgen
package require readcharmmtop
package require solvate
package require autoionize

  lappend topfiles [file join $env(CHARMMTOPDIR) top_all36_prot.rtf]
  lappend topfiles [file join $env(CHARMMTOPDIR) top_all36_lipid.rtf]
  lappend topfiles [file join $env(CHARMMTOPDIR) top_all36_na.rtf]
  lappend topfiles [file join $env(CHARMMTOPDIR) top_all36_carb.rtf]
  lappend topfiles [file join $env(CHARMMTOPDIR) top_all36_cgenff.rtf]
  lappend topfiles [file join $env(CHARMMTOPDIR) toppar_all36_carb_glycopeptide.str]
  lappend topfiles [file join $env(CHARMMTOPDIR) toppar_water_ions_namd.str]

pdbalias ...

segment AP1 {pdb A04.pdb
              first NTER
              last CTER}
 patch CYSD AP1:5
 patch CYSD AP1:8
 patch CYSD AP1:26
 patch CYSD AP1:29
 patch CYSD AP1:50
 patch CYSD AP1:55
 patch CYSD AP1:72
 patch CYSD AP1:16
 patch CYSD AP1:19

segment B01 {pdb B04.pdb
              auto none}
segment DNA1 {pdb D04.pdb
              first 5PHO
              last 3PHO }
segment ENA2 {pdb E04.pdb
              first 5PHO
              last 3PHO }
segment Z LSB04a.psf01 {pdb Z04.pdb}
segment M01 {pdb M04.pdb}
regenerate angles dihedrals
coordpdb A04.pdb AP1
coordpdb B04.pdb B01
coordpdb D04.pdb DNA1
coordpdb E04.pdb ENA2
coordpdb M04.pdb M01
coordpdb Z04.pdb Z01
writepdb LSB04.pdb
writepsf LSB04.psf

As you can see, I have a ligand, two RNA chains, Mg, and Zn atoms the later which require the CYSD patch.
The equivalent AUTOPSF script for VMD is:

mol new LSB04.pdb
autopsf -mol 0 -solvate -ionize -prefix LSB04a -patch CYSD AP1:5 -patch CYSD AP1:8 -patch CYSD AP1:16 -patch CYSD AP1:19 -patch CYSD AP1:26 -patch CYSD AP1:29 -patch CYSD AP1:50 -patch CYSD AP1:55 -patch CYSD AP1:72
solvate LSB04a.psf LSB04a.pdb -t 25 -o LSB04aw25
autoionize -psf LSB04aw25.psf -pdb LSB04aw25.pdb -sc 0.15 -o LSB04aw25i
writepdb LSB04aw25i.pdb
writepsf LSB04aw25i.psf

What is the issue with PSFGEN? Is the toppology 'INP' hard encoded to be top_all27_prot_lipid_na.inp ?
Also AUTOPSF will only use 3TER and 5TER MeO on the RNA not 3PHO, 5PHO terminations.

Best regards,

Mark Andrew White, Ph.D.
Associate Professor of Biochemistry & Molecular Biology,
Manager, SCSB Macromolecular X-ray Laboratory
6.658A Basic Sciences, UTMB, Galveston, TX