|
|||||||||||||||||||||||||||||||||
AMBER Archive (2004)Subject: Re: Re: Re: Re: Re: AMBER: a question about Van der waals radius
From: Ye Mei (ymei_at_itcc.nju.edu.cn)
3.2 The Algorithm
The algorithm for locating hydrogen bonds involves two steps. Firstly,
Cysteines are treated specially. Any two Cysteines which have their
==============================================================================
Donors
1. N (ie Main Chain NHs of recognised residues)
2. CYH SG, HIS NE2, HIS ND1, LYS NZ, ASN ND2, GLN NE2, ARG NE, ARG NH1,
3. Recognised donors of non-standard recognised molecules
4. Nitrogen atoms in unrecognised molecules
5. Oxygen atoms of recognised water molecules
Acceptors
1. O (ie Main Chain COs of recognised amino - not imino - acid residues)
2. CYH SG, CSS SG, ASP OD1, ASP OD2, GLU OE1, GLU OE2, HIS ND1, MET SD,
3. Recognised acceptors of non-standard recognised molecules
4. Oxygen atoms in HETATM molecules (including waters)
Atoms that may act as both donors and acceptors under the -X or -x options
1. HIS CD2, HIS CE1, ASN OD1, ASN ND2, GLN OE1, GLN NE2
Non-Standard Recognised Molecules
1. Standard Nucleotides C, A, U, G, T, also ATP.
2. Coenzymes COA, FMN, HEM, NAD
3. Small Molecules MTX, ACE, FOR
4. Amino Acids AIB, PHL, SEC, ALM, MPR, FRD, LYM, GLM, PPH, PGL, OLE, ABA,
These can be listed with the -P option.
-----------------------------------------------------------------------
| |||||||||||||||||||||||||||||||||
|