Dear all
I simulated a protein-protein complex using Amber20 for 100ns. The system
consists of a dimer complexed with two copies of the same protein. I used a
cubic water box. When I ran autoimage using AmberTools18, till ~50ns, the
trajectory is fine. However, beyond that, there seems to be some imaging
issues. I am just not able to solve this.
Can someone please help me?
The input files that I have tried are:
Trial1
trajin 6md.cdf
autoimage
trajout imaged6.nc netcdf
Trial2
trajin 6md.cdf
autoimage
trajout imaged6.nc netcdf nobox
Trial3
trajin 6md.cdf
center :1-199 origin mass
image origin center
center :1-398 origin mass
image origin center
center :1-576 origin mass
image origin center
image origin center
center :1-754
trajout imaged6.nc netcdf
(1-199 is one monomer of protein1, 200 to 398 is monomer 2 of protein 1,
399 to 576 and 577 to 754 are the two copies of the partner protein)
Thanks
Suchetana Gupta
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Received on Tue Oct 06 2020 - 00:30:02 PDT
