Dear amber users
*Happy new year*
I'm beginner in amber.
I want analyse hydrogen bonds by ptarj.
my system contains protein, dna and water. I want to study water mediated
hydrogen bonds
(occupancy, lifetime) between protein and dna.
Should this be done in two stages? 1) ptraj input file contains protein and
water donors/acceptors.
2) ptraj input file contains dna and water donors/acceptors.
if so, for example, for stage 1, Which of the following two ptraj input
files is more suitable (protein has 60 residues)?
**************************************************************************************************************************************
A)>>>>>>>>>
trajin md.mdcrd
#-- Donors from standard amino acids
donor mask :GLN.NE2
donor mask :ASN.ND2
donor mask :TYR.OH
donor mask :ASP.OD1
donor mask :ASP.OD2
donor mask :GLU.OE1
donor mask :GLU.OE2
#-- Acceptors from standard amino acids
acceptor mask :LYS.NZ :LYS.HZ1
acceptor mask :LYS.NZ :LYS.HZ2
acceptor mask :LYS.NZ :LYS.HZ3
acceptor mask :ARG.NH2 :ARG.HH21
acceptor mask :ARG.NH2 :ARG.HH22
acceptor mask :ARG.NH1 :ARG.HH11
acceptor mask :ARG.NH1 :ARG.HH12
acceptor mask :ARG.NE :ARG.HE
acceptor mask :ASN.ND2 :ASN.HD21
acceptor mask :ASN.ND2 :ASN.HD22
acceptor mask :GLN.NE2 :GLN.HE21
acceptor mask :GLN.NE2 :GLN.HE22
#-- Backbone donors and acceptors for this particular molecule
# N-H for prolines do not exist so are not in the mask
#
donor mask 1-60.O
acceptor mask :2-60.N :2-60.H
#Terminal residues have different atom names
donor mask .OXT
acceptor mask :1.N :1.H1
acceptor mask :1.N :1.H2
acceptor mask :1.N :1.H3
hbond print .05 series out hb.out
solventdonor WAT O
solventacceptor WAT O H1
solventacceptor WAT O H2
*********************************************
B)>>>>>>>>>
trajin md.mdcrd
#-- Donors from standard amino acids
donor mask :WAT.O
donor mask :GLN.NE2
donor mask :ASN.ND2
donor mask :TYR.OH
donor mask :ASP.OD1
donor mask :ASP.OD2
donor mask :GLU.OE1
donor mask :GLU.OE2
#-- Acceptors from standard amino acids
acceptor mask :WAT.O :WAT.H1
acceptor mask :WAT.O :WAT.H2
acceptor mask :LYS.NZ :LYS.HZ1
acceptor mask :LYS.NZ :LYS.HZ2
acceptor mask :LYS.NZ :LYS.HZ3
acceptor mask :ARG.NH2 :ARG.HH21
acceptor mask :ARG.NH2 :ARG.HH22
acceptor mask :ARG.NH1 :ARG.HH11
acceptor mask :ARG.NH1 :ARG.HH12
acceptor mask :ARG.NE :ARG.HE
acceptor mask :ASN.ND2 :ASN.HD21
acceptor mask :ASN.ND2 :ASN.HD22
acceptor mask :GLN.NE2 :GLN.HE21
acceptor mask :GLN.NE2 :GLN.HE22
#-- Backbone donors and acceptors for this particular molecule
# N-H for prolines do not exist so are not in the mask
#
donor mask 1-60.O
acceptor mask :2-60.N :2-60.H
#Terminal residues have different atom names
donor mask .OXT
acceptor mask :1.N :1.H1
acceptor mask :1.N :1.H2
acceptor mask :1.N :1.H3
hbond print .05 series out hb.out
****************************************************************************
If only the number of water molecules to be consider, what to do?
*****************************************************************************
otherwise, What should ptraj input file be included?
I have a general question, please explain more about usage of mask in
determination of acceptors and donors.
any help will highly appreciated.
Best regards
--
Leila Karami
Ph.D. student of Physical Chemistry
K.N. Toosi University of Technology
Theoretical Physical Chemistry Group
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Sun Jan 02 2011 - 07:30:04 PST
