VMD-L Mailing List

From: Steven(Yuhang) Wang (ywang148_at_illinois.edu)
Date: Fri Jan 06 2017 - 11:12:14 CST

Hi Jim,

Thank you for clarifying the issue.

Steven

On 1/6/2017 10:53 AM, Jim Phillips wrote:
>
> 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
>>