[gmx-users] Regarding top2psf script

Justin Lemkul jalemkul at vt.edu
Thu Apr 18 12:41:30 CEST 2013

On 4/18/13 5:15 AM, Venkat Reddy wrote:
> Dear all,
> I want to reverse transform my CG lipid system to AA. I have been using
> g_fg2cg but I am getting some errors (like "Atoms in the .top are not
> numbered consecutively from 1"). So, I intend to use the script
> top2psf.plwritten by Dr.Lemkul, so that I can avail the help of VMD in
> cg2aa
> conversion. Can we use it for pure lipid systems (say
> POPC+CHOL+triglyceride+CE)?
> When I tried to execute it, I am getting the following error
>   "Cannot open angles for reading: No such file or directory"

My script only works on a single molecule topology.  It will not work for a 
complex system like yours.  Perhaps you can process each .itp file separately, 
which may be of some use, but that will only potentially give you an AA 
representation of a single molecule.



Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080


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