Dear amber users,
I`m tryng to set up a Simulated Annealing calculation for a protein-ligand complex. In some tutorials and posts I have seen examples of SA inputs in which NMR restraints (through DISANG file) is used to avoid system to blowup or chiralities inversions at very high temperatures. However, I also have seen cases in which NMR restraints are not used even at 800 K.
In SA, from which temperature on NMR restraints is recommended to be used?
If I understood the section 6.7 of Amber 11 manual, in absence of experimental data, the chiralities restraints are the only ones I can get (using makeCHIR_RST) to use as a DISANG file, right?
According to the manual, I "may have to edit the output of this program to change trans peptide constraints to cis, as appropriate". How can I check and change that?
Thanks in advance,
Josmar Rocha
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Received on Thu Jan 12 2012 - 14:30:03 PST
