VMD-L Mailing List

From: Wang, Steven (ywang148_at_illinois.edu)
Date: Wed Jan 04 2017 - 16:57:19 CST

I was using VMD 1.9.3 autoionize to add ions to my system. The output looks fine except for the following parsing error printed on the terminal:

psfgen) Toplogy and parameter information for water and ions.
psfgen)
psfgen) reading topology from stream file
psfgen) Topology for water and ions
psfgen)
psfgen) 31 1
psfgen) Parameters for water and ions
psfgen)
psfgen) ERROR! Failed to parse atom statement. Line 152: ATOMS

psfgen) duplicate type key HT
psfgen) duplicate type key HX
psfgen) duplicate type key OT
psfgen) duplicate type key OX
psfgen) duplicate type key LIT
psfgen) duplicate type key SOD
psfgen) duplicate type key MG
psfgen) duplicate type key POT
psfgen) duplicate type key CAL
psfgen) duplicate type key RUB
psfgen) duplicate type key CES
psfgen) duplicate type key BAR
psfgen) duplicate type key ZN
psfgen) duplicate type key CAD
psfgen) duplicate type key CLA
psfgen) ERROR! Failed to parse bond statement. Line 169: BONDS

psfgen) ERROR! FAILED TO RECOGNIZE HT. Line 178: HT HT 0.0 1.5139 ! from TIPS3P geometry (for SHAKE w/PARAM)

psfgen) ERROR! FAILED TO RECOGNIZE HT. Line 179: HT OT 450.0 0.9572 ! from TIPS3P geometry

psfgen) ERROR! FAILED TO RECOGNIZE OX. Line 180: OX HX 545.0 0.9700 ! hydroxide ion

psfgen) ERROR! Failed to parse angle statement. Line 182: ANGLES

psfgen) ERROR! FAILED TO RECOGNIZE HT. Line 195: HT OT HT 55.0 104.52 ! FROM TIPS3P GEOMETRY

psfgen) ERROR! Failed to parse dihedral statement. Line 197: DIHEDRALS

psfgen) ERROR! Failed to parse improper statement. Line 210: IMPROPER

psfgen) ERROR! FAILED TO RECOGNIZE NONBONDED. Line 221: NONBONDED nbxmod 5 atom cdiel shift vatom vdistance vswitch -

psfgen) ERROR! FAILED TO RECOGNIZE CUTNB. Line 222: cutnb 14.0 ctofnb 12.0 ctonnb 10.0 eps 1.0 e14fac 1.0 wmin 1.5

psfgen) ERROR! FAILED TO RECOGNIZE HT. Line 225: HT 0.0 -0.046 0.2245

psfgen) ERROR! FAILED TO RECOGNIZE OT. Line 226: OT 0.0 -0.1521 1.7682

psfgen) ERROR! FAILED TO RECOGNIZE OX. Line 229: OX 0.000000 -0.120000 1.700000 ! ALLOW POL ION

psfgen) ERROR! FAILED TO RECOGNIZE HX. Line 231: HX 0.000000 -0.046000 0.224500 ! ALLOW PEP POL SUL ARO ALC

psfgen) ERROR! FAILED TO RECOGNIZE LIT. Line 235: LIT 0.0 -0.00233 1.2975 ! Lithium

psfgen) ERROR! FAILED TO RECOGNIZE SOD. Line 237: SOD 0.0 -0.0469 1.41075 ! new CHARMM Sodium

psfgen) ERROR! FAILED TO RECOGNIZE MG. Line 239: MG 0.0 -0.0150 1.18500 ! Magnesium

psfgen) ERROR! FAILED TO RECOGNIZE POT. Line 241: POT 0.0 -0.0870 1.76375 ! Potassium

psfgen) ERROR! FAILED TO RECOGNIZE CAL. Line 243: CAL 0.0 -0.120 1.367 ! Calcium

psfgen) ERROR! FAILED TO RECOGNIZE RUB. Line 245: RUB 0.0000 -0.15 1.90 ! Rubidium

psfgen) ERROR! FAILED TO RECOGNIZE CES. Line 247: CES 0.0 -0.1900 2.100 ! Cesium

psfgen) ERROR! FAILED TO RECOGNIZE BAR. Line 249: BAR 0.0 -0.150 1.890 ! Barium

psfgen) ERROR! FAILED TO RECOGNIZE ZN. Line 251: ZN 0.000000 -0.250000 1.090000 ! Zinc

psfgen) ERROR! FAILED TO RECOGNIZE CAD. Line 253: CAD 0.000000 -0.120000 1.357000 ! Cadmium

psfgen) ERROR! FAILED TO RECOGNIZE CLA. Line 255: CLA 0.0 -0.150 2.27 ! Chloride

psfgen) ERROR! FAILED TO RECOGNIZE NBFIX. Line 258: NBFIX

psfgen) ERROR! FAILED TO RECOGNIZE SOD. Line 261: SOD CLA -0.083875 3.731 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189

psfgen) ERROR! FAILED TO RECOGNIZE POT. Line 262: POT CLA -0.114236 4.081 ! From osmotic pressure calibration, J. Phys.Chem.Lett. 1:183-189

psfgen) NBFix between carboxylate and sodium
psfgen)
psfgen) skipping statements at end of file due to end or return statement
psfgen) building segment ION
psfgen) setting patch for first residue to NONE
psfgen) setting patch for last residue to NONE

Steven