VMD-L Mailing List

From: Steven(Yuhang) Wang (ywang148_at_illinois.edu)
Date: Wed Jan 04 2017 - 20:08:33 CST

Hi Ciacomo,

Thank you for the suggestion and thanks for the quick response.

Steven

On 1/4/2017 6:57 PM, 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
> <mailto: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
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>
> /"As computer programmers we have a responsibility to make sure that
> we run the computers instead of the computers running us."/ - Steve
> Oualline
>
>