Hello everyone,
I've been trying to use ptraj to analyze the hydrogen bonding in a peptide
system, and I've noticed something unusual in the mask processing.
My system is the peptide AAHAFLHR. After running MD, I want to look at the
global hydrogen bonding, so I used the hbond_ptraj.in input file taken from
Ross Walker's tutorial:
analyse_hbond.ptraj-----------------------------------
trajin pep.mdcrd 1 200
#-- Donors from standard amino acids
donor mask :GLN.OE1
donor mask :GLN.NE2
donor mask :ASN.OD1
donor mask :ASN.ND2
donor mask :TYR.OH
donor mask :ASP.OD1
donor mask :ASP.OD2
donor mask :GLU.OE1
donor mask :GLU.OE2
donor mask :SER.OG
donor mask :THR.OG1
donor mask :HIS.ND1
donor mask :HIE.ND1
donor mask :HID.NE2
#-- Acceptors from standard amino acids
acceptor mask :ASN.ND2 :ASN.HD21
acceptor mask :ASN.ND2 :ASN.HD22
acceptor mask :TYR.OH :TYR.HH
acceptor mask :GLN.NE2 :GLN.HE21
acceptor mask :GLN.NE2 :GLN.HE22
acceptor mask :TRP.NE1 :TRP.HE1
acceptor mask :LYS.NZ :LYS.HZ1
acceptor mask :LYS.NZ :LYS.HZ2
acceptor mask :LYS.NZ :LYS.HZ3
acceptor mask :SER.OG :SER.HG
acceptor mask :THR.OG1 :THR.HG1
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 :HIS.NE2 :HIS.HE2
acceptor mask :HIE.NE2 :HIE.HE2
acceptor mask :HID.ND1 :HID.HD1
acceptor mask :HIP.ND1,NE2 :HIP.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 .O
acceptor mask :2-8.N :2-8.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
#-- 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 pep_hbond.out
------------------------------------------end analyse_hbond.ptraj
When I ran $ ptraj pep.prmtop analyse_hbond.ptraj
there were some surprising results involving the masks. Of course, most of
the masks corresponded to no atoms, because this is a peptide that only
contains six distinct residue types. However, there were several masks that
picked up on atoms that they weren't supposed to. Specifically, :GLN.NE2,
:HIE.ND1, :HID.NE2, :ASN.HD21, :ASN.HD22, :TRP.HE1, :SER.HG, :HIS.HE2,
:HIE.NE2, :HIE.HE2, :HID.ND1, :HID.HD1, :HIP.ND1,NE2, and :HIP.HD1,HE2 all
found atoms that don't actually exist in the file. All of these atom names
*do* exist in my system, but they are not on these residues. Most of these
didn't impact things, but several led to incorrect analysis. Because of the
misread :HID.ND1 mask, the (protonated) ND1 atom of my His residues were
treated as H-bond acceptors as well as donors. Also, because ptraj included
the Phe HE2 atom in the :HIS.HE2 mask, the N and H atoms no longer matched,
and ptraj ignored any His NE2-HE2 H-bond donation.
I am very puzzled by the way that the masks are handled. It's looks like
any residue names that don't exist in the system are simply erase (e.g.
ptraj is treating :GLN.NE2 as simply .NE2). Any idea what's going on here?
Amber8 Module: ptraj
Read in control variables
Read in atom names...
Read in charges...
Read in masses...
Read in IAC (atoms involved in L-J)...
Read in NUMEX (index to excl atom list)...
Read in NNO (index for nonbond of .type)...
Read in residue labels...
ALA ALA HIE ALA PHE LEU HIE ARG
Read in the residue to atom pointer list...
Read in bond parameters RK and REQ...
Read in angle parameters TK and TEQ...
Read in dihedral parameters PK, PN and PHASE...
Read in SOLTY...
Read in L-J parameters CN1 and CN2...
Read in info for bonds w/ hydrogen...
Read in info for bonds w/out hydrogen...
Read in info for angles w/ hydrogen...
Read in info for angles w/out hydrogen...
Read in info for dihedrals w/ hydrogen...
Read in info for dihedrals w/out hydrogen...
Read in excluded atom list...
Read in h-bond parameters: AG, BG, and HBCUT...
Read in atomic symbols (types)...
Read in tree information...
Read in the JOIN info...
Read in the IROTAT info...
Successfully completed readParm.
PTRAJ: Processing input file...
Input is from file analyse_hbond.ptraj
PTRAJ: trajin pep.mdcrd 1 200
Checking coordinates: pep.mdcrd
PTRAJ: donor mask :GLN.OE1
Mask [:GLN.OE1] represents 0 atoms !!!NO ATOMS DETECTED!!!
WARNING in ptraj, donor: No atoms selected (:GLN.OE1), ignoring...
PTRAJ: donor mask :GLN.NE2
Mask [:GLN.NE2] represents 2 atoms
PTRAJ: donor mask :ASN.OD1
Mask [:ASN.OD1] represents 0 atoms !!!NO ATOMS DETECTED!!!
WARNING in ptraj, donor: No atoms selected (:ASN.OD1), ignoring...
PTRAJ: donor mask :ASN.ND2
Mask [:ASN.ND2] represents 0 atoms !!!NO ATOMS DETECTED!!!
WARNING in ptraj, donor: No atoms selected (:ASN.ND2), ignoring...
PTRAJ: donor mask :TYR.OH
Mask [:TYR.OH] represents 0 atoms !!!NO ATOMS DETECTED!!!
WARNING in ptraj, donor: No atoms selected (:TYR.OH), ignoring...
PTRAJ: donor mask :ASP.OD1
Mask [:ASP.OD1] represents 0 atoms !!!NO ATOMS DETECTED!!!
WARNING in ptraj, donor: No atoms selected (:ASP.OD1), ignoring...
PTRAJ: donor mask :ASP.OD2
Mask [:ASP.OD2] represents 0 atoms !!!NO ATOMS DETECTED!!!
WARNING in ptraj, donor: No atoms selected (:ASP.OD2), ignoring...
PTRAJ: donor mask :GLU.OE1
Mask [:GLU.OE1] represents 0 atoms !!!NO ATOMS DETECTED!!!
WARNING in ptraj, donor: No atoms selected (:GLU.OE1), ignoring...
PTRAJ: donor mask :GLU.OE2
Mask [:GLU.OE2] represents 0 atoms !!!NO ATOMS DETECTED!!!
WARNING in ptraj, donor: No atoms selected (:GLU.OE2), ignoring...
PTRAJ: donor mask :SER.OG
Mask [:SER.OG] represents 0 atoms !!!NO ATOMS DETECTED!!!
WARNING in ptraj, donor: No atoms selected (:SER.OG), ignoring...
PTRAJ: donor mask :THR.OG1
Mask [:THR.OG1] represents 0 atoms !!!NO ATOMS DETECTED!!!
WARNING in ptraj, donor: No atoms selected (:THR.OG1), ignoring...
PTRAJ: donor mask :HIS.ND1
Mask [:HIS.ND1] represents 2 atoms
PTRAJ: donor mask :HIE.ND1
Mask [:HIE.ND1] represents 2 atoms
PTRAJ: donor mask :HID.NE2
Mask [:HID.NE2] represents 2 atoms
PTRAJ: acceptor mask :ASN.ND2 :ASN.HD21
Mask [:ASN.ND2] represents 0 atoms !!!NO ATOMS DETECTED!!!
Mask [:ASN.HD21] represents 1 atoms
WARNING in ptraj, acceptor: No heavy atom was selected (:ASN.ND2),
ignoring...
WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
atom selection in the two masks :ASN.ND2 and :ASN.HD21 which contain 0 and 1
atoms respectively. Ignoring...
PTRAJ: acceptor mask :ASN.ND2 :ASN.HD22
Mask [:ASN.ND2] represents 0 atoms !!!NO ATOMS DETECTED!!!
Mask [:ASN.HD22] represents 1 atoms
WARNING in ptraj, acceptor: No heavy atom was selected (:ASN.ND2),
ignoring...
WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
atom selection in the two masks :ASN.ND2 and :ASN.HD22 which contain 0 and 1
atoms respectively. Ignoring...
PTRAJ: acceptor mask :TYR.OH :TYR.HH
Mask [:TYR.OH] represents 0 atoms !!!NO ATOMS DETECTED!!!
Mask [:TYR.HH] represents 0 atoms !!!NO ATOMS DETECTED!!!
WARNING in ptraj, acceptor: No heavy atom was selected (:TYR.OH),
ignoring...
WARNING in ptraj, acceptor: No hydrogen atom was selected (:TYR.HH),
ignoring...
PTRAJ: acceptor mask :GLN.NE2 :GLN.HE21
Mask [:GLN.NE2] represents 2 atoms
Mask [:GLN.HE21] represents 0 atoms !!!NO ATOMS DETECTED!!!
WARNING in ptraj, acceptor: No hydrogen atom was selected (:GLN.HE21),
ignoring...
WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
atom selection in the two masks :GLN.NE2 and :GLN.HE21 which contain 2 and 0
atoms respectively. Ignoring...
PTRAJ: acceptor mask :GLN.NE2 :GLN.HE22
Mask [:GLN.NE2] represents 2 atoms
Mask [:GLN.HE22] represents 0 atoms !!!NO ATOMS DETECTED!!!
WARNING in ptraj, acceptor: No hydrogen atom was selected (:GLN.HE22),
ignoring...
WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
atom selection in the two masks :GLN.NE2 and :GLN.HE22 which contain 2 and 0
atoms respectively. Ignoring...
PTRAJ: acceptor mask :TRP.NE1 :TRP.HE1
Mask [:TRP.NE1] represents 0 atoms !!!NO ATOMS DETECTED!!!
Mask [:TRP.HE1] represents 3 atoms
WARNING in ptraj, acceptor: No heavy atom was selected (:TRP.NE1),
ignoring...
WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
atom selection in the two masks :TRP.NE1 and :TRP.HE1 which contain 0 and 3
atoms respectively. Ignoring...
PTRAJ: acceptor mask :LYS.NZ :LYS.HZ1
Mask [:LYS.NZ] represents 0 atoms !!!NO ATOMS DETECTED!!!
Mask [:LYS.HZ1] represents 0 atoms !!!NO ATOMS DETECTED!!!
WARNING in ptraj, acceptor: No heavy atom was selected (:LYS.NZ),
ignoring...
WARNING in ptraj, acceptor: No hydrogen atom was selected (:LYS.HZ1),
ignoring...
PTRAJ: acceptor mask :LYS.NZ :LYS.HZ2
Mask [:LYS.NZ] represents 0 atoms !!!NO ATOMS DETECTED!!!
Mask [:LYS.HZ2] represents 0 atoms !!!NO ATOMS DETECTED!!!
WARNING in ptraj, acceptor: No heavy atom was selected (:LYS.NZ),
ignoring...
WARNING in ptraj, acceptor: No hydrogen atom was selected (:LYS.HZ2),
ignoring...
PTRAJ: acceptor mask :LYS.NZ :LYS.HZ3
Mask [:LYS.NZ] represents 0 atoms !!!NO ATOMS DETECTED!!!
Mask [:LYS.HZ3] represents 0 atoms !!!NO ATOMS DETECTED!!!
WARNING in ptraj, acceptor: No heavy atom was selected (:LYS.NZ),
ignoring...
WARNING in ptraj, acceptor: No hydrogen atom was selected (:LYS.HZ3),
ignoring...
PTRAJ: acceptor mask :SER.OG :SER.HG
Mask [:SER.OG] represents 0 atoms !!!NO ATOMS DETECTED!!!
Mask [:SER.HG] represents 1 atoms
WARNING in ptraj, acceptor: No heavy atom was selected (:SER.OG),
ignoring...
WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
atom selection in the two masks :SER.OG and :SER.HG which contain 0 and 1
atoms respectively. Ignoring...
PTRAJ: acceptor mask :THR.OG1 :THR.HG1
Mask [:THR.OG1] represents 0 atoms !!!NO ATOMS DETECTED!!!
Mask [:THR.HG1] represents 0 atoms !!!NO ATOMS DETECTED!!!
WARNING in ptraj, acceptor: No heavy atom was selected (:THR.OG1),
ignoring...
WARNING in ptraj, acceptor: No hydrogen atom was selected (:THR.HG1),
ignoring...
PTRAJ: acceptor mask :ARG.NH2 :ARG.HH21
Mask [:ARG.NH2] represents 1 atoms
Mask [:ARG.HH21] represents 1 atoms
PTRAJ: acceptor mask :ARG.NH2 :ARG.HH22
Mask [:ARG.NH2] represents 1 atoms
Mask [:ARG.HH22] represents 1 atoms
PTRAJ: acceptor mask :ARG.NH1 :ARG.HH11
Mask [:ARG.NH1] represents 1 atoms
Mask [:ARG.HH11] represents 1 atoms
PTRAJ: acceptor mask :ARG.NH1 :ARG.HH12
Mask [:ARG.NH1] represents 1 atoms
Mask [:ARG.HH12] represents 1 atoms
PTRAJ: acceptor mask :ARG.NE :ARG.HE
Mask [:ARG.NE] represents 1 atoms
Mask [:ARG.HE] represents 1 atoms
PTRAJ: acceptor mask :HIS.NE2 :HIS.HE2
Mask [:HIS.NE2] represents 2 atoms
Mask [:HIS.HE2] represents 3 atoms
WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
atom selection in the two masks :HIS.NE2 and :HIS.HE2 which contain 2 and 3
atoms respectively. Ignoring...
PTRAJ: acceptor mask :HIE.NE2 :HIE.HE2
Mask [:HIE.NE2] represents 2 atoms
Mask [:HIE.HE2] represents 2 atoms
PTRAJ: acceptor mask :HID.ND1 :HID.HD1
Mask [:HID.ND1] represents 2 atoms
Mask [:HID.HD1] represents 1 atoms
WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
atom selection in the two masks :HID.ND1 and :HID.HD1 which contain 2 and 1
atoms respectively. Ignoring...
PTRAJ: acceptor mask :HIP.ND1,NE2 :HIP.HE2,HD1
Mask [:HIP.ND1,NE2] represents 4 atoms
Mask [:HIP.HE2,HD1] represents 4 atoms
PTRAJ: donor mask .O
Mask [.O] represents 8 atoms
PTRAJ: acceptor mask :2-8.N :2-8.H
Mask [:2-8.N] represents 7 atoms
Mask [:2-8.H] represents 7 atoms
PTRAJ: donor mask .OXT
Mask [.OXT] represents 1 atoms
PTRAJ: acceptor mask :1.N :1.H1
Mask [:1.N] represents 1 atoms
Mask [:1.H1] represents 1 atoms
PTRAJ: acceptor mask :1.N :1.H2
Mask [:1.N] represents 1 atoms
Mask [:1.H2] represents 1 atoms
PTRAJ: acceptor mask :1.N :1.H3
Mask [:1.N] represents 1 atoms
Mask [:1.H3] represents 1 atoms
PTRAJ: hbond print .05 series hbt out pep_hbond.out
FYI: No output trajectory specified (trajout), none will be saved.
PTRAJ: Successfully read the input file.
Coordinate processing will occur on 200 frames.
Summary of I/O and actions follows:
INPUT COORDINATE FILES
File (pep.mdcrd) is an AMBER trajectory with 200 sets
OUTPUT COORDINATE FILE
NULL entry
ACTIONS
1> HBOND saved to series hbt, output to file pep_hbond.out,
data will be sorted, intra-residue interactions will NOT be included,
Distance cutoff is 3.00 angstroms, angle cutoff is 120.00 degrees
Hydrogen bond information will be dumped for occupancies > 0.05
Estimated memory usage for this hbond call: 0.64 MB
donors: 13 acceptors: 21
Processing AMBER trajectory file pep.mdcrd
Set 1 .................................................
Set 50 .................................................
Set 100 .................................................
Set 150 .................................................
Set 200
PTRAJ: Successfully read in 200 sets and processed 200 sets.
Dumping accumulated results (if any)
PTRAJ HBOND dumping summary to file pep_hbond.out
-----------------------------------------------------------------------
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Received on Sun Aug 19 2007 - 06:07:12 PDT
