Hi all! I wonder if there is an example for proper topology and parameter treatment for phosphorylated-serine residue available that works with the protein_1.0.top and protein_1.0.par files that come with xplor-nih-2.37? I have examples from other sources but the charges/distances etc. are treated slightly different overall from the above two files.
Also I saw that there are examples for protein-DNA complex and prot-prot docking in the /eginput folder. I wonder if there is also a protein-peptide example available? The prot-prot docking protocol relies much on the input structures, and I wanted to take into account more of the peptide flexibility. Much appreciation in advance for any help! Best regards, Yuan
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