VMD-L Mailing List

From: Peter Freddolino (petefred_at_ks.uiuc.edu)
Date: Thu May 17 2007 - 11:21:41 CDT

Hi Javier,
in the usual lipid topology file for charmm, dppc comes in three pieces:
The head group/glycerol piece ) (PCGL) and (for DPPC) two palmitic acid
pieces (PALM). You need to use the EST1 and EST2 patches to combine
them; please see the comments in the topology file for details. You may
find it easier to create your own DPPC topology entry and rename the
residues in your pdb accordingly.
Peter

Lechuga, Javier wrote:
> Hello,
>
> In order to use the attached "DPPC.pdb" into NAMD, I would need to
> generate its psf format file (I have attached the tcl script and the
> topology file I am using).
>
> I wonder if someone can tell me why I am not getting correct results
> after executing the command line: vmd -dispdev text -e "PsfGen
> DPPC.tcl". The lipid seems to be in three pieces (Head and tails) at
> the obtained file. It does not look like that when I open the original
> file with VMD.
>
> Thank you