AMBER: Bug in ptraj mask processing?

From: Steve Spronk <spronk.umich.edu>
Date: Wed, 15 Aug 2007 15:18:15 -0400

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



-----------------------------------------------------------------------
The AMBER Mail Reflector
To post, send mail to amber.scripps.edu
To unsubscribe, send "unsubscribe amber" to majordomo.scripps.edu
Received on Sun Aug 19 2007 - 06:07:12 PDT
Custom Search