Re: problem with solvating a structure

From: Udaya Dahal (dahal.udaya_at_gmail.com)
Date: Tue Feb 26 2019 - 15:38:45 CST

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
>

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