I am a new comer of AMBER, and I want to calculate free energy change
with sander TI (AMBER8), but I have some "simple" questions, so, could
you help me?
1) How to tell leap that certain atoms disappeared? For
example, when val changes to ala, I change the methyls (CT,HC,HC,HC) to
hydrogens (HC, DH,DH,DH ), followed the steps in this page:
http://web.njit.edu/all_topics/Prog_Lang_Docs/html/amber7/gibbs_box/HTML/xleap_edit_selected.html
but when I want to saveamberparmpert, leap told me that could not find
the perturbed type "DH".
2) How to calculate the delta.charge? Also in
that page, the delta.charge of first CB is set to 0.1050, how to get
this value?
Thanks in advance!
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Received on Mon Jun 28 2004 - 20:53:00 PDT
