From: Peter Freddolino (petefred_at_umich.edu)
Date: Tue May 22 2018 - 21:43:40 CDT

Can you send either the command line that you used to run autoionize or a
screenshot of the gui state (depending on whether you ran in the gui or
text mode)? How did you generate the psf/pdb combination that you are
giving to autoionize? Your system has an odd non-integer charge going in...
Best,
Peter

On Tue, May 22, 2018 at 3:58 PM, Mani Kandan <manikandand5110_at_gmail.com>
wrote:

> 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--000000000000a6b55b056cd680d7--