Re: problem with solvating a structure

From: João Ribeiro (jribeiro_at_ks.uiuc.edu)
Date: Tue Feb 26 2019 - 15:33:42 CST

Hi Hadi,

please reply to all so other users can benefit from the discussion. I was
actually referring to the lines printed right after you executed the
command. Those seem to be already in the middle of the process.
like one following the lines below: "
psfgen) reading structure from psf file test1.psf
psfgen) reading coordinates from pdb file test1.pdb

Seems like psfgen is not recognizing your structure. How did you build your
structure?

Best

João

On Tue, Feb 26, 2019 at 3:14 PM Hadi Rahmaninejad <ha.rahmaani_at_gmail.com>
wrote:

> Ok, sorry about that. In the VMD TkConsole I got a lot of warning like
> this:
> "psfgen) Warning: failed to set coordinate for atom SI XXXX:26
> SURF"
>
> and this is a part of pdb and psf file that was generated for me:
> "ATOM 293 O XXXXS 8 0.000 0.000 0.000 -1.00 0.00
> SURF
> ATOM 294 O XXXXS 8 0.000 0.000 0.000 -1.00 0.00
> SURF
> ATOM 295 O XXXXS 8 0.000 0.000 0.000 -1.00 0.00
> SURF
> ATOM 296 O XXXXS 8 0.000 0.000 0.000 -1.00 0.00
> SURF"
> and
> " 1 SURF 1 XXXX O OC23 -0.550000 15.9994 0
> 2 SURF 1 XXXX O OC23 -0.550000 15.9994 0
> 3 SURF 1 XXXX O OC23 -0.550000 15.9994 0
> 4 SURF 1 XXXX O OC23 -0.550000 15.9994 0
> 5 SURF 1 XXXX O OC23 -0.550000 15.9994 0"
> are these information that you meant I post?
>
>
> On Tue, Feb 26, 2019 at 3:48 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
>>
>

-- 
……………………………………………………...
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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