Re: problem with solvating a structure

From: Hadi Rahmaninejad (ha.rahmaani_at_gmail.com)
Date: Wed Feb 27 2019 - 10:04:07 CST

Thank you for the clarification.

On Tue, Feb 26, 2019 at 4:38 PM Udaya Dahal <dahal.udaya_at_gmail.com> wrote:

> Hi Hadi,
>
> That means psfgen is not reading your silica structure properly, sometimes
> the correct pdb format is required ( with segnane column).
>
> You will see the lot of error messages for each silica atom. I had similar
> issue and putting segname had solved my issue.
>
> Regards,
>
> On Tue, Feb 26, 2019 at 3:49 PM João Ribeiro <jribeiro_at_ks.uiuc.edu> wrote:
>
>> Dear Hadi,
>>
>> For future reference, questions related to VMD and its plugins should be
>> posted in the vmd-l_at_ks.uiuc.edu mailing list.
>>
>> Now, answering your question, VMD prints a lot of useful information in
>> the terminal window. Would it be possible for you to post the messages
>> print to the terminal after you executed the solvated command?
>>
>> Best
>>
>> João
>>
>>
>> On Tue, Feb 26, 2019 at 2:35 PM Hadi Rahmaninejad <ha.rahmaani_at_gmail.com>
>> wrote:
>>
>>> Hello Dear NAMD users,
>>>
>>> I am using psfgen in VMD TkConsole in order to solvate a silica
>>> structure containing mostly Si and O atoms with water. The command I am
>>> using are:
>>> "solvate silica.psf silica.pdb -t 10"
>>> However, the result is a pdb file in which the coordinate of most of Si
>>> and O is "zero" (0.000). and so the vmd shows a weird structure of one Si
>>> connected to few oxygen and Hydrogen surrounded by water molecules. I
>>> highly appreciate if anybody can help me with this.
>>>
>>> Thank you in advance,
>>> Hadi
>>>
>>
>>
>> --
>> ……………………………………………………...
>> João Vieira Ribeiro
>> Theoretical and Computational Biophysics Group
>> Beckman Institute, University of Illinois
>> http://www.ks.uiuc.edu/~jribeiro/
>> jribeiro_at_ks.uiuc.edu
>> +1 (217) 3005851
>>
> --
> Sent from Gmail Mobile
>

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