VMD-L Mailing List

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Tue May 22 2018 - 13:43:05 CDT

Please keep the vmd-l in the thread, so other users can benefit from the
conversation.

Which VMD version are you using? Does this error occur if you use the VMD
1.9.4 alpha version? Did you, by any chance, change the
/toppar_water_ions_namd.str
file the readcharmmtop1.2 folder?

Best

João

On Tue, May 22, 2018 at 2:32 PM Mani Kandan <manikandand5110_at_gmail.com>
wrote:

> Following details are shown in TK console and it has some psfgen error
> also.
>
>
>
> psfgen) clearing structure, preserving topology and aliases
> Autoionize) Reading sin_hex.psf/sin_hex.pdb...
> psfgen) clearing structure, preserving topology and aliases
> psfgen) reading structure from psf file sin_hex.psf
> psfgen) psf file does not contain cross-terms
> psfgen) reading coordinates from pdb file sin_hex.pdb
> Autoionize) System net charge before adding ions: -6.535188674926758e.
> Autoionize) Ions to be placed:
> Autoionize) 260 POT
> Autoionize) 260 CLA
> Autoionize) Required min distance from molecule: 5A.
> Autoionize) Required min distance between ions: 5A.
> Autoionize) Output file prefix 'sin_ions'.
> Autoionize) Ions will be added to segname ION.
> Autoionize) Obtained positions for 520 ions.
> Autoionize) Tagged 520 water molecules for deletion.
> Autoionize) Deleted 520 water molecules.
> Autoionize) Reading CHARMM topology file...
> psfgen) reading topology file
> /home/manikandan/Programs/vmd/lib/plugins/noarch/tcl/readcharmmtop1.2/toppar_water_ions_namd.str
>
> 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--000000000000b4d3fa056ccfca13--