VMD-L Mailing List

From: Mani Kandan (manikandand5110_at_gmail.com)
Date: Tue May 22 2018 - 13:46:29 CDT

I am using vmd 1.9.3 version. I didn't change anything in that files and I
am using the binary version of vmd 1.9.3.

With Regards,

MANIKANDAN D

On Wed, May 23, 2018 at 12:13 AM, João Ribeiro <jribeiro_at_ks.uiuc.edu> wrote:

> 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.
>> 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
>> psfgen) Info: generating structure...segment complete.
>> Autoionize) Randomizing ion positions...
>> Autoionize) Assigning ion coordinates...
>> psfgen) Info: writing psf file sin_ions.psf
>> psfgen) total of 54441 atoms
>> psfgen) total of 49642 bonds
>> psfgen) total of 13387 angles
>> psfgen) total of 0 dihedrals
>> psfgen) total of 0 impropers
>> psfgen) total of 0 explicit exclusions
>> psfgen) total of 0 cross-terms
>> psfgen) Info: psf file complete.
>> psfgen) Info: writing pdb file sin_ions.pdb
>> psfgen) Info: pdb file complete.
>> Autoionize) Loading new system with added ions...
>> Autoionize) System net charge after adding ions: -6.535188674926758e.
>> Autoionize) WARNING: System has a non-integer total charge. There was
>> likely a problem in the process of building it.
>> Autoionize) All done.
>>
>>
>> On Tue, May 22, 2018 at 11:55 PM, João Ribeiro <jribeiro_at_ks.uiuc.edu>
>> wrote:
>>
>>> Dear Manikandan,
>>>
>>> could you please send the information printed to the VMD terminal window
>>> when you used the plugin?
>>>
>>> Thank you
>>>
>>> Best
>>>
>>> João
>>>
>>> On Tue, May 22, 2018 at 1:45 PM Mani Kandan <manikandand5110_at_gmail.com>
>>> wrote:
>>>
>>>> Hi all,
>>>>
>>>> I had a system of water molecules of number 55605 (Including H1, H2,
>>>> OH2 before using the plugin). After adding 260 POT and 260 CLA ions using
>>>> the plugin, the number of water molecules has to be 55085 ( 55605-260-260)
>>>> but it shows 40161. How this possible?
>>>>
>>>> Actually, autoionize plugin replaces water molecules into ions then why
>>>> I am having reduced number of water molecules?
>>>>
>>>>
>>>> With Regards,
>>>>
>>>> MANIKANDAN D
>>>>
>>>>
>>>
>>> --
>>> ……………………………………………………...
>>> João Vieira Ribeiro
>>> Theoretical and Computational Biophysics Group
>>> Beckman Institute, University of Illinois
>>> jribeiro_at_ks.uiuc.edu
>>> +1 (217) 3005851
>>>
>>
>>
>
> --
> ……………………………………………………...
> João Vieira Ribeiro
> Theoretical and Computational Biophysics Group
> Beckman Institute, University of Illinois
> jribeiro_at_ks.uiuc.edu
> +1 (217) 3005851
>