VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Mon Dec 17 2012 - 10:30:47 CST

On Mon, Dec 17, 2012 at 3:52 PM, yp sun <sunyeping_at_yahoo.com.cn> wrote:

> Dear VMD users,
>
> I try to use vmd to insert a protein into lipid membrane using the scrpit
> combine.tcl, and I type the following command:
>
> vmd -dispdev text -e combine.tcl
>
> I got the following error message:
>
> Warning) Detected a mismatch between CUDA runtime and GPU driver
> Warning) Check to make sure that GPU drivers are up to date.
> Info) No CUDA accelerator devices available.
> Info) No joysticks found. Joystick interface disabled.
> Info) Dynamically loaded 69 plugins in directory:
> Info) C:/Program Files/University of Illinois/VMD/plugins/WIN32/molfile
> 1.6
> ERROR: Unable to open topology file top_all27_prot_lipid.inp
>

here is the key problem. where is this file?
you may need to adjust the script or provide the file.

> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> psfgen) clearing structure, preserving topology and aliases
> psfgen) reading structure from psf file membrane.psf
> psfgen) psf file does not contain cross-terms
> psfgen) reading coordinates from pdb file membrane.pdb
> ERROR: Unable to open psf file protein.psf
> MOLECULE DESTROYED BY FATAL ERROR! Use resetpsf to start over.
> MOLECULE MISSING! Use resetpsf to start over.
>
> temp
> MOLECULE MISSING! Use resetpsf to start over.
> MOLECULE MISSING! Use resetpsf to start over.
> ERROR) Could not read file temp.psf
> Unable to load structure file temp.psf
> There is no 'top' molecule in atomselect's 'molId'
> can't read "sellip": no such variable
> can't read "lseglist": no such variable
> -55
> 41
> -51
> 34
> There is no 'top' molecule in atomselect's 'molId'
> MOLECULE MISSING! Use resetpsf to start over.
> MOLECULE MISSING! Use resetpsf to start over.
> Info) VMD for WIN32, version 1.9.1 (February 1, 2012)
> Info) Exiting normally.
> vmd > Couldn't open psf file temp.psf
>
>
> Does these mean that my computer cannot do the inserting job? Is there any
> resolution for this problem? Thank you!
>
>
you have to pay attention to error messages, and particularly
the first message. everything else is just errors resulting from
the previous failed operation(s).

axel.

> Yeping Sun
> CAS Key Laboratory of Pathogenic Microbiology & Immunology
> INSTITUTE OF MICROBIOLOGY CHINESE ACADEMY OF SCIENCES
> NO.1 Beichen West Road,Chaoyang District,Beijing 100101,china
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
International Centre for Theoretical Physics, Trieste. Italy.