AMBER Archive (2006)

Subject: AMBER: rmsd value for organic molecule

From: Varsha Goyal (
Date: Mon Apr 24 2006 - 14:00:20 CDT

Dear Amber users,
In tutorial5 we have equilibriated sustiva. But after
that if we want to calculate rmsd value how we do
that. I tired to use the dame way we do for protein
but i am getting bus error
Here is my ptraj file:

trajin md1.mdcrd
trajin md2.mdcrd
trajin md3.mdcrd
trajin md4.mdcrd
trajin md5.mdcrd
trajin md6.mdcrd
trajin md7.mdcrd
trajin md8.mdcrd
trajin md9.mdcrd
trajin md10.mdcrd
trajin md11.mdcrd
trajin md12.mdcrd
trajin md13.mdcrd
trajin md14.mdcrd
trajin md15.mdcrd
trajin md16.mdcrd
trajin md17.mdcrd
trajin md18.mdcrd
trajin md19.mdcrd
trajin md20.mdcrd
trajin md21.mdcrd

rms reference out rmsd_lowest_energy.dat @N,S,O time
after reading md21.mdcrd
i get following error
"Bus error"

i believe that it is because of atom type we define
after @.
I used gaff to define atom types
if i define gaff atom types it still doesn't work

If anyone knows the solution please help me.

Varsha Gupta

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