Hi
I have a homodimer protein (each dimer has 99 residues), which during my
periodic box-simulations (explicit waters) separated. I then tried
Imaging using the following command:
trajin wt.restrt_2500
trajout wt2500imaged pdb
center :1-99 origin
image :100-198 origin center
go
I also tried:
trajin wt.restrt_2500
trajout wt2500imaged pdb
center :1-99
image :100-198 center
go
The dimers do reform, but the problem is that now there are hugh VDW
contacts between atoms. For example, I have an Oxygen from one monomer
that is 1.97A to a Nitrogen of the other monomer.
I checked the MD energy and so there is no "clashing" between the atoms
during MD. The problem only occurs when I do the "imaging".
Any help would be greatly appreciated
Cheers, Steve
-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Fri Jul 30 2004 - 20:53:00 PDT
