AMBER: About TI with sander

From: Chunhu Tan <tanc.uci.edu>
Date: Mon, 28 Jun 2004 12:35:54 -0700

 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
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