[gmx-users] g_rama, g_chi for polymer structure

Mark Abraham Mark.Abraham at anu.edu.au
Thu Apr 22 08:16:09 CEST 2010

On 22/04/10 15:09, Yongchul Chung wrote:
> Dear gmx-users,
> I want to construct the Ramachandran Plot for the molecules I am
> simulating -- 100 polyethylene chain (n=16). But when I do $ g_rama, I
> get "Found 0 phi-psi combinations" message. The problem seems to me that
> when I ran the simulation initially, I didn't have dihedral information
> listed on *.itp file of my molecule as well as on *.top file.

The .top file contains a [ molecules ] section which refers to [ 
moleculetypes ] sections, which may either be in that file or #included 
from an .itp file. The latter is equivalent to a textual cut-and-paste. 
Either of these approaches leads to the same result.

I think the real problem is that phi and psi are definitions that 
require the existence of protein backbone, and you don't have one.

> However, I
> created angle.ndx file manually with 4 carbon atoms grouped together and
> can invoke g_angle command to get other dihedral data I want. I
> encounter similar error(?) message "Found 0 phi-psi combinations" while
> invoking g_chi command.
> I think I can play around with g_angle data and get what I want
> eventually, but I wonder if I can fully utilize what is already
> implemented in GROMACS for my polymer structure.

It is not clear to me what functionality (might) exist for proteins that 
is transferable to your case, nor that using g_angle (and friends) with 
artfully constructed index groups is not a better approach anyway.


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