AMBER Archive (2006)

Subject: AMBER: hbond analysis2

From: Claire Zerafa (cporteli_at_waldonet.net.mt)
Date: Tue Jul 04 2006 - 09:00:35 CDT

Hi Amber users,

Further to my posting fro yesterday, I have a hond analysis scipt as
follows:

trajin /DATA/DIETHYLSTILBOESTROL_DYNAMICS/diethyl2-10.binpos

#-- Donors from standard amino acids
donor mask :GLN_at_OE1
donor mask :GLN_at_NE2
donor mask :ASN_at_OD1
donor mask :ASN_at_ND2
donor mask :TYR_at_OH
donor mask :ASP_at_OD1
donor mask :ASP_at_OD2
donor mask :GLU_at_OE1
donor mask :GLU_at_OE2
donor mask :SER_at_OG
donor mask :THR_at_OG1
donor mask :HIS_at_ND1
donor mask :HIE_at_ND1
donor mask :HID_at_NE2

#-- Acceptors from standard amino acids
acceptor mask :ASN_at_ND2 :ASN_at_HD21
acceptor mask :ASN_at_ND2 :ASN_at_HD22
acceptor mask :TYR_at_OH :TYR_at_HH
acceptor mask :GLN_at_NE2 :GLN_at_HE21
acceptor mask :GLN_at_NE2 :GLN_at_HE22
acceptor mask :TRP_at_NE1 :TRP_at_HE1
acceptor mask :LYS_at_NZ :LYS_at_HZ1
acceptor mask :LYS_at_NZ :LYS_at_HZ2
acceptor mask :LYS_at_NZ :LYS_at_HZ3
acceptor mask :SER_at_OG :SER_at_HG
acceptor mask :THR_at_OG1 :THR_at_HG1
acceptor mask :ARG_at_NH2 :ARG_at_HH21
acceptor mask :ARG_at_NH2 :ARG_at_HH22
acceptor mask :ARG_at_NH1 :ARG_at_HH11
acceptor mask :ARG_at_NH1 :ARG_at_HH12
acceptor mask :ARG_at_NE :ARG_at_HE
acceptor mask :HIS_at_NE2 :HIS_at_HE2
acceptor mask :HIE_at_NE2 :HIE_at_HE2
acceptor mask :HID_at_ND1 :HID_at_HD1
acceptor mask :HIP_at_ND1,NE2 :HIP_at_HE2,HD1

#-- Backbone donors and acceptors for this particular molecule
# N-H for prolines do not exist so are not in the mask

donor mask :BEN 1_at_O7 :1_at_H5
donor mask :BEN 1_at_O20 :1_at_H20
 

acceptor mask :BEN 1_at_O7 :1_at_H5
acceptor mask :BEN 1_at_O20 :1_at_H20

#Terminal residues have different atom names
donor mask @OXT
acceptor mask :1_at_N :1_at_H1
acceptor mask :1_at_N :1_at_H2
acceptor mask :1_at_N :1_at_H3

#-- series hbt is just a placeholder to ensure we get the full analysis.
If you don't
#have the word series you don't get a full analysis.
hbond print .05 series hbt out
/DATA/DIETHYLSTILBOESTROL_TRAJECTORY_ANALYSIS/diethyl_hbond_analysis.dat
go

I have 2 problems:

I am still not sure that I am identifying the donor and acceptor OH on
the steroid correctly
The programm stalls while reading the aa donor and acceptor sites. It
continues to run, but no more output is written, and I get a getargument
error. I have changed format from mdrcd to binpos to aid memory, but I
have already gotten outputs, so I dont think it is a memory issue...

any ideas pls??

thanks

cxx

-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber_at_scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo_at_scripps.edu