VMD-L Mailing List

From: Mihaela Drenscko (quo.physics_at_gmail.com)
Date: Thu Nov 06 2014 - 12:47:34 CST

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:

PSF

        1 !NTITLE

 REMARKS VMD-generated NAMD/X-Plor PSF structure
file

      237 !NATOM

       1 PCL 1 PCLH OE OHL -0.639542
  15.9994 0

       2 PCL 1 PCLH H1E HOL 0.387133
   1.0079 0

       3 PCL 1 PCLH CE CTL2 0.340824
  12.0107 0

       4 PCL 1 PCLH H2E HAL2 -0.055905
   1.0079 0

       5 PCL 1 PCLH H3E HAL2 0.021503
   1.0079 0

And after move, psf of pcl looked like this:

PSF

        1 !NTITLE

 REMARKS VMD-generated NAMD/X-Plor PSF structure
file

      237 !NATOM

       1 PCL 1 PCLH OE OE 0.000000
  15.9990 0

       2 PCL 1 PCLH H1E H1E 0.000000
   1.0080 0

       3 PCL 1 PCLH CE CE 0.000000
  12.0110 0

       4 PCL 1 PCLH H2E H2E 0.000000
   1.0080 0

       5 PCL 1 PCLH H3E H3E 0.000000
   1.0080 0

I see that atom types have been replaced by atom names.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

Thank you,
Mihaela