VMD-L Mailing List

From: Mani Kandan (manikandand5110_at_gmail.com)
Date: Tue May 22 2018 - 14:58:21 CDT

Now I tried VMD 1.9.4 version, their psfgen errors are fixed but Number of
water molecules and ions are not balanced (i.e discussed in already). I am
solvated the system using solvate plugin. After solvate, I got many water
molecules with same segid and resid. How can I solve that?

With Regards,

MANIKANDAN D

On Wed, May 23, 2018 at 12:48 AM, João Ribeiro <jribeiro_at_ks.uiuc.edu> wrote:

> The latest VMD 1.9.4 version has the psfgen error fixed.
>
> Regarding the number of atoms, please make sure that the waters have
> unique segment names. If more two water molecules sharing the same segid
> and resid, both molecules will be deleted during the replacement of the
> waters by the ions.
>
> Best
>
> João
>
>
> On Tue, May 22, 2018 at 2:46 PM Mani Kandan <manikandand5110_at_gmail.com>
> wrote:
>
>> 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
>>>
>>
>>
>
> --
> ……………………………………………………...
> João Vieira Ribeiro
> Theoretical and Computational Biophysics Group
> Beckman Institute, University of Illinois
> jribeiro_at_ks.uiuc.edu
> +1 (217) 3005851
>