AMBER Archive (2005)

Subject: AMBER: How to calculate hydrogen bond involved with water molecules quickly?

From: haixiao jin (jinhx952_at_gmail.com)
Date: Mon Aug 08 2005 - 00:07:48 CDT

Here is my input file for calculate hydrogen bond involved with water molecules.

Hbond1.in (the oxygen of water molecules is donor, and the hydrogen of
residues is acceptor)
trajin 1npt.mdcrd
center :1-347 origin mass
image origin center familiar
donor mask :345_at_O
donor mask :346_at_O
donor mask :347_at_O
acceptor ARG NE HE
acceptor ARG NH1 HH11
acceptor ARG NH1 HH12
acceptor ARG NH2 HH21
acceptor ARG NH2 HH22
acceptor ASN ND2 HD21
acceptor ASN ND2 HD22
acceptor CYS SG HG
acceptor GLN NE2 HE21
acceptor GLN NE2 HE22
acceptor HID ND1 HD1
acceptor SER OG HG
acceptor THR OG1 HG1
acceptor TYR OH HH
acceptor ALA N H
acceptor ARG N H
acceptor ASN N H
acceptor ASP N H
acceptor CYS N H
acceptor GLN N H
acceptor GLU N H
acceptor GLY N H
acceptor HIS N H
acceptor ILE N H
acceptor LEU N H
acceptor LYS N H
acceptor MET N H
acceptor PHE N H
acceptor PRO N H
acceptor SER N H
acceptor THR N H
acceptor TRP N H
acceptor TYR N H
acceptor VAL N H
hbond distance 3.5 angle 120.0 donor acceptor neighbor 2 series hbond

this file has been run without any problem. However, running hbond2.in
(the hydrogen of water molecules is acceptor and the heteroatom of
residues is donor) has obtained a empty result. Here is the hbond2.in
file

trajin 1npt.mdcrd
center :1-347 origin mass
image origin center familiar
donor mask :ALA_at_N,O
donor mask :ARG_at_N,O,NE,NH1,NH2
donor mask :ASN_at_N,O,OD1,ND2
donor mask :ASP_at_N,O,OD1,OD2
donor mask :CYS_at_N,O,SG
donor mask :GLN_at_N,O,OE1,NE2
donor mask :GLU_at_N,O,OE1,OE2
donor mask :GLY_at_N,O
donor mask :HIS_at_N,O,ND1
donor mask :ILE_at_N,O
donor mask :LEU_at_N,O
donor mask :LYS_at_N,O
donor mask :MET_at_N,O,SD
donor mask :PHE_at_N,O
donor mask :PRO_at_N,O
donor mask :SER_at_N,O,OG
donor mask :THR_at_N,O,OG1
donor mask :TRP_at_N,O
donor mask :TYR_at_N,O,OH
donor mask :VAL_at_N,O
acceptor mask :345_at_O H1
acceptor mask :345_at_O H2
acceptor mask :346_at_O H1
acceptor mask :346_at_O H2
acceptor mask :347_at_O H1
acceptor mask :347_at_O H2
hbond distance 3.5 angle 120.0 donor acceptor neighbor 2 series hbond

is the expression of acceptor in hbond2.in right? I have been try
"acceptor WAT O H1" and "acceptor WAT O H2" in hbond2.in, It fails due
to low internal memory. Any suggestion will be appreciated !
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