VMD-L Mailing List

From: Jim Phillips (jim_at_ks.uiuc.edu)
Date: Fri Jan 06 2017 - 10:53:40 CST

I just wanted to point out that psfgen *can* read stream files. For some
reason in the toppar_water_ions_namd.str file shipped with VMD the "read
para" lines are commented out so the parameter section is not skipped.

In any case, you can ignore the ERROR messages below that are clearly due
to unrecognized lines in the parameter section.

Jim

On Wed, 4 Jan 2017, Giacomo Fiorin wrote:

> Hello Steven, it looks like the CHARMM-readable stream file has been added
> to the version of autoionize. The stream file is distributed as-is by the
> MacKerell lab due to the NBFIX corrections for ion-charged molecule
> interactions, but is not readable by psfgen.
>
> The quick solution in your case would be to replace the stream file that
> autoionize reads (the path will be shown earlier) with a RTF file (you
> don't need NBFIX records during system construction).
>
> Copying here the VMD developers address to address the issue in the plugin
> distribution.
>
> Giacomo
>
> On Wed, 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
>>
>
>
>
> --
> Giacomo Fiorin
> Associate Professor of Research
> Institute for Computational Molecular Science (ICMS)
> College of Science and Technology, Temple University
> 1925 North 12th Street (035-07), Room 704D
> Philadelphia, PA 19122-1801
> Phone: +1-215-204-4213
>
> Scholar: http://goo.gl/Q3TBQU
> Personal: http://giacomofiorin.github.io/
> Lab page: https://icms.cst.temple.edu/members.html
>
> *"As computer programmers we have a responsibility to make sure that we run
> the computers instead of the computers running us."* - Steve Oualline
>