VMD-L Mailing List

From: Steven(Yuhang) Wang (ywang148_at_illinois.edu)
Date: Wed Jan 04 2017 - 20:20:33 CST

Hi Peter,

Here is the command I used:

autoionize -psf $psf -pdb $pdb \
         -sc $concentration -cation $cation -anion $anion \
         -o $output_prefix -from $ion_solute_distance -between
$ion_ion_distance \
         -seg $segname

The variables were defined earlier in my script.

Just as a side note, I also tried the same script with VMD 1.9.2. No
parsing error encountered there.

Steven

On 1/4/2017 8:11 PM, Peter Freddolino wrote:
> Could you perhaps give the autoionize command that you tried…?
>
>> On Jan 4, 2017, at 9:10 PM, Steven(Yuhang) Wang <ywang148_at_illinois.edu> wrote:
>>
>> Hi Peter,
>>
>> I tried both the GUI and the command line version, both encountered the same problem. The input structure was prepared using psfgen (command line version).
>>
>> Steven
>>
>>
>> On 1/4/2017 8:01 PM, Peter Freddolino wrote:
>>> It would help if you gave a bit more information — did you use the gui or command line version? How did you obtain your input structure?
>>>
>>>> On Jan 4, 2017, at 5:57 PM, Wang, Steven <ywang148_at_illinois.edu> wrote:
>>>>
>>>> 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