Dear Amber users,
I need your help in setting up a membrane-bound protein which also contains
an ATP-Mg complex in its structure.
I prepared the input files using CHARMM-GUI, but when I try to run a
simulation using those files, the system is blowing up during the first
step of equilibration.
After few blow-ups I managed to successfully run an MD simulation of the
whole protein, membrane, water and ions, but without the ATP-Mg complex. I
got a short production run in which I did not see anything weird. So I
believe that the MD simulation crashes because of the ATP parameters I'm
using.
However, when I used the ATP.frcmod file I got from CHARMM-GUI and used the
pdb file containing the ATP complex and Mg ion, I managed to run the
simulation as well; I got the trajectories from a production run.
I am attaching my .mdout file from the failed equilibration.
I could really need some help in getting this system running.
Looking forward to your help.
Best, Karolina
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Received on Thu Jul 20 2023 - 05:30:02 PDT
