error in openbabel

Python Prescription - Virtual Screening Tool

[PyRx is no longer developed at MGL]

Moderator: sargis

Forum rules
[PyRx is no longer developed at MGL]

error in openbabel

Postby IMANE » Mon May 25, 2015 10:29 am

Hello Sargis,
I had installed PyRx version 0.8 in window 8.But when I used openbabel to convert the file from sdf to pbdqt and for energy minimization there have an error : vtkOpenGLTexture (13DB0468): No scalar values found for texture input! can you help me?
Thank You for answering

Regards
Imane
User avatar
IMANE
Millimolar User
Millimolar User
 
Posts: 4
Joined: Tue Mar 24, 2015 3:57 pm

Re: error in openbabel

Postby sargis » Mon May 25, 2015 6:20 pm

Hello Imane,

Thank you for using PyRx. If you can send me the sdf file and steps to reproduce this, I'll looking into it.

Regards,
Sargis
User avatar
sargis
Picomolar User
Picomolar User
 
Posts: 583
Joined: Fri Oct 17, 2008 10:39 pm

Re: error in openbabel

Postby IMANE » Tue May 26, 2015 8:24 am

Hi Sargis,
Thank you for your response, you will find the sdf file attached to this e-mail .
Attachments
sdf.sdf
(14.84 KiB) Downloaded 151 times
User avatar
IMANE
Millimolar User
Millimolar User
 
Posts: 4
Joined: Tue Mar 24, 2015 3:57 pm

Re: error in openbabel

Postby sargis » Wed May 27, 2015 3:36 am

IMANE wrote:Hi Sargis,
Thank you for your response, you will find the sdf file attached to this e-mail .

Hi Imane,
You are welcome. When I looked at it, all atoms were on top of each other. You can open it with a text editor and see that all coordinates are zero. Where did you get that file? PyRx needs 2D or 3D coordinates before it can do energy minimization.
User avatar
sargis
Picomolar User
Picomolar User
 
Posts: 583
Joined: Fri Oct 17, 2008 10:39 pm

Re: error in openbabel

Postby IMANE » Wed May 27, 2015 10:29 am

hi sargis,
I get this file by converting smiles to sdf file using openbabel. here is the smiles :
S1CCN=C1NC(=O)c1c2[nH]cc(c2c(F)cc1)C(=O)C(=O)N1CCN(CC1)C(=O)c1ncccc1
s1ccnc1NC(=O)c1c2[nH]cc(c2c(F)cc1)C(=O)C(=O)N1CCN(CC1)C(=O)c1ncccc1
s1cc(nc1NC(=O)c1c2[nH]cc(c2c(F)cc1)C(=O)C(=O)N1CCN(CC1)C(=O)c1ncccc1)C
Fc1c2c([nH]cc2C(=O)C(=O)N2CCN(CC2)C(=O)c2ncccc2)c(cc1)C(=O)Nc1[nH]c2c(n1)cccc2
User avatar
IMANE
Millimolar User
Millimolar User
 
Posts: 4
Joined: Tue Mar 24, 2015 3:57 pm


Return to PyRx

Who is online

Users browsing this forum: No registered users and 4 guests