AMBER Archive (2009)

Subject: [AMBER] GAFF and NME, ACE terminal res

From: Jio M (jiomm_at_yahoo.com)
Date: Mon Jul 13 2009 - 15:51:06 CDT

Dear AMBER users ,

I am new to AMBER though I was going through Advanced Amber tutorial Tutorial 1 using dye and linker.

I want to make same type of residues to be protected by NMe (for C terminal) or ACE(N terminal). pls clarify the following:

1) can I use GAFF for these residues to be used later and making prmtop file.

2) I cannot use other than HF/631-G* method to optimise. the charges
that I will use, during RESP fit, for NMe and ACE (as given in
tutorial) are actually derived by optimising amino acids by HF/631-G*
method also.

but for GAFF parameters have been derived by using MP2/631-G (will this
effect the charges so derived by HF method during simulation). this is
confusion pls clarify it whether I can use GAFF or not or  I have
misunderstood the things

thanks in advance

JIomm

      
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