Dear Amber Fans
I built one of these carbon structures with hydroxyl groups and optimized
it with Gauss-16. I then used these structures as ligands for a protein. In
leap suite, I got only 22 warnings. When I saved both prmtop and inpcrd
files, I got the following message
1-4: angle 2862 2898 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 2859 2898 duplicates bond ('triangular' bond) or angle ('square'
bond)
1-4: angle 2859 2862 duplicates bond ('triangular' bond) or angle ('square'
bond)
The problem is during minimization, steepest descent is only working and
during heating the energy of the system is very fluctuating. I have amber
16 and my system is 8 core processor and operating system is ubuntu
18.04_64x.
I can not understand what is this message means.
Any suggestions, please let me know
said
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Received on Mon Oct 08 2018 - 12:00:02 PDT
