VMD-L Mailing List

From: Axel Kohlmeyer (akohlmey_at_gmail.com)
Date: Thu Nov 06 2014 - 22:23:45 CST

On Thu, Nov 6, 2014 at 7:47 PM, Mihaela Drenscko <quo.physics_at_gmail.com> wrote:
> Hello,
>
> I am running a simulation of pcl in popc membrane with water. I get the
> error:
> FATAL ERROR: DIDN'T FIND vdW PARAMETER FOR ATOM TYPE OE
>
> I must mention that I moved (using moveby in vmd) pcl from coordinates
> outside the popc water box to inside the cell.
> Before move, the psf file for pcl looked like this:

[...[

> I see that atom types have been replaced by atom names. Where is my mistake,
> or how do I prevent this change from happening?

what would be even more troubling is the fact that your second file
also is lacking information of the charges and possibly other pieces
of information. most likely you created this psf file from a file
*without* this information, e.g. a PDB file.

however, the real problem is in that grey mass between your ears. PSF
files do not contain any coordinate information, so saving a PSF file
after moving atoms around is *completely* pointless. the topology
information of a compound doesn't change because of some translation
or rotation.
this is at the core of how MD codes like CHARMM and NAMD and many
others work. unless you realize and recognize this and understand the
consequences, you will have a *lot* of trouble with even the most
simple operations.

axel.

> Thank you,
> Mihaela
> 

-- 
Dr. Axel Kohlmeyer  akohlmey_at_gmail.com  http://goo.gl/1wk0
College of Science & Technology, Temple University, Philadelphia PA, USA
International Centre for Theoretical Physics, Trieste. Italy.