AMBER Archive (2007)

Subject: AMBER: Bug in ptraj mask processing?

From: Steve Spronk (spronk_at_umich.edu)
Date: Wed Aug 15 2007 - 14:18:15 CDT

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_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 @O

acceptor mask :2-8_at_N :2-8_at_H

#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 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_at_NE2,
:HIE_at_ND1, :HID_at_NE2, :ASN_at_HD21, :ASN_at_HD22, :TRP_at_HE1, :SER_at_HG, :HIS_at_HE2,
:HIE_at_NE2, :HIE_at_HE2, :HID_at_ND1, :HID_at_HD1, :HIP_at_ND1,NE2, and :HIP_at_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_at_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_at_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_at_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_at_OE1

Mask [:GLN_at_OE1] represents 0 atoms !!!NO ATOMS DETECTED!!!

WARNING in ptraj, donor: No atoms selected (:GLN_at_OE1), ignoring...

 

PTRAJ: donor mask :GLN_at_NE2

Mask [:GLN_at_NE2] represents 2 atoms

 

PTRAJ: donor mask :ASN_at_OD1

Mask [:ASN_at_OD1] represents 0 atoms !!!NO ATOMS DETECTED!!!

WARNING in ptraj, donor: No atoms selected (:ASN_at_OD1), ignoring...

 

PTRAJ: donor mask :ASN_at_ND2

Mask [:ASN_at_ND2] represents 0 atoms !!!NO ATOMS DETECTED!!!

WARNING in ptraj, donor: No atoms selected (:ASN_at_ND2), ignoring...

 

PTRAJ: donor mask :TYR_at_OH

Mask [:TYR_at_OH] represents 0 atoms !!!NO ATOMS DETECTED!!!

WARNING in ptraj, donor: No atoms selected (:TYR_at_OH), ignoring...

 

PTRAJ: donor mask :ASP_at_OD1

Mask [:ASP_at_OD1] represents 0 atoms !!!NO ATOMS DETECTED!!!

WARNING in ptraj, donor: No atoms selected (:ASP_at_OD1), ignoring...

 

PTRAJ: donor mask :ASP_at_OD2

Mask [:ASP_at_OD2] represents 0 atoms !!!NO ATOMS DETECTED!!!

WARNING in ptraj, donor: No atoms selected (:ASP_at_OD2), ignoring...

 

PTRAJ: donor mask :GLU_at_OE1

Mask [:GLU_at_OE1] represents 0 atoms !!!NO ATOMS DETECTED!!!

WARNING in ptraj, donor: No atoms selected (:GLU_at_OE1), ignoring...

 

PTRAJ: donor mask :GLU_at_OE2

Mask [:GLU_at_OE2] represents 0 atoms !!!NO ATOMS DETECTED!!!

WARNING in ptraj, donor: No atoms selected (:GLU_at_OE2), ignoring...

 

PTRAJ: donor mask :SER_at_OG

Mask [:SER_at_OG] represents 0 atoms !!!NO ATOMS DETECTED!!!

WARNING in ptraj, donor: No atoms selected (:SER_at_OG), ignoring...

 

PTRAJ: donor mask :THR_at_OG1

Mask [:THR_at_OG1] represents 0 atoms !!!NO ATOMS DETECTED!!!

WARNING in ptraj, donor: No atoms selected (:THR_at_OG1), ignoring...

 

PTRAJ: donor mask :HIS_at_ND1

Mask [:HIS_at_ND1] represents 2 atoms

 

PTRAJ: donor mask :HIE_at_ND1

Mask [:HIE_at_ND1] represents 2 atoms

 

PTRAJ: donor mask :HID_at_NE2

Mask [:HID_at_NE2] represents 2 atoms

 

PTRAJ: acceptor mask :ASN_at_ND2 :ASN_at_HD21

Mask [:ASN_at_ND2] represents 0 atoms !!!NO ATOMS DETECTED!!!

Mask [:ASN_at_HD21] represents 1 atoms

WARNING in ptraj, acceptor: No heavy atom was selected (:ASN_at_ND2),
ignoring...

WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the

atom selection in the two masks :ASN_at_ND2 and :ASN_at_HD21 which contain 0 and 1

atoms respectively. Ignoring...

 

PTRAJ: acceptor mask :ASN_at_ND2 :ASN_at_HD22

Mask [:ASN_at_ND2] represents 0 atoms !!!NO ATOMS DETECTED!!!

Mask [:ASN_at_HD22] represents 1 atoms

WARNING in ptraj, acceptor: No heavy atom was selected (:ASN_at_ND2),
ignoring...

WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the

atom selection in the two masks :ASN_at_ND2 and :ASN_at_HD22 which contain 0 and 1

atoms respectively. Ignoring...

 

PTRAJ: acceptor mask :TYR_at_OH :TYR_at_HH

Mask [:TYR_at_OH] represents 0 atoms !!!NO ATOMS DETECTED!!!

Mask [:TYR_at_HH] represents 0 atoms !!!NO ATOMS DETECTED!!!

WARNING in ptraj, acceptor: No heavy atom was selected (:TYR_at_OH),
ignoring...

WARNING in ptraj, acceptor: No hydrogen atom was selected (:TYR_at_HH),
ignoring...

 

PTRAJ: acceptor mask :GLN_at_NE2 :GLN_at_HE21

Mask [:GLN_at_NE2] represents 2 atoms

Mask [:GLN_at_HE21] represents 0 atoms !!!NO ATOMS DETECTED!!!

WARNING in ptraj, acceptor: No hydrogen atom was selected (:GLN_at_HE21),
ignoring...

WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the

atom selection in the two masks :GLN_at_NE2 and :GLN_at_HE21 which contain 2 and 0

atoms respectively. Ignoring...

 

PTRAJ: acceptor mask :GLN_at_NE2 :GLN_at_HE22

Mask [:GLN_at_NE2] represents 2 atoms

Mask [:GLN_at_HE22] represents 0 atoms !!!NO ATOMS DETECTED!!!

WARNING in ptraj, acceptor: No hydrogen atom was selected (:GLN_at_HE22),
ignoring...

WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the

atom selection in the two masks :GLN_at_NE2 and :GLN_at_HE22 which contain 2 and 0

atoms respectively. Ignoring...

 

PTRAJ: acceptor mask :TRP_at_NE1 :TRP_at_HE1

Mask [:TRP_at_NE1] represents 0 atoms !!!NO ATOMS DETECTED!!!

Mask [:TRP_at_HE1] represents 3 atoms

WARNING in ptraj, acceptor: No heavy atom was selected (:TRP_at_NE1),
ignoring...

WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the

atom selection in the two masks :TRP_at_NE1 and :TRP_at_HE1 which contain 0 and 3

atoms respectively. Ignoring...

 

PTRAJ: acceptor mask :LYS_at_NZ :LYS_at_HZ1

Mask [:LYS_at_NZ] represents 0 atoms !!!NO ATOMS DETECTED!!!

Mask [:LYS_at_HZ1] represents 0 atoms !!!NO ATOMS DETECTED!!!

WARNING in ptraj, acceptor: No heavy atom was selected (:LYS_at_NZ),
ignoring...

WARNING in ptraj, acceptor: No hydrogen atom was selected (:LYS_at_HZ1),
ignoring...

 

PTRAJ: acceptor mask :LYS_at_NZ :LYS_at_HZ2

Mask [:LYS_at_NZ] represents 0 atoms !!!NO ATOMS DETECTED!!!

Mask [:LYS_at_HZ2] represents 0 atoms !!!NO ATOMS DETECTED!!!

WARNING in ptraj, acceptor: No heavy atom was selected (:LYS_at_NZ),
ignoring...

WARNING in ptraj, acceptor: No hydrogen atom was selected (:LYS_at_HZ2),
ignoring...

 

PTRAJ: acceptor mask :LYS_at_NZ :LYS_at_HZ3

Mask [:LYS_at_NZ] represents 0 atoms !!!NO ATOMS DETECTED!!!

Mask [:LYS_at_HZ3] represents 0 atoms !!!NO ATOMS DETECTED!!!

WARNING in ptraj, acceptor: No heavy atom was selected (:LYS_at_NZ),
ignoring...

WARNING in ptraj, acceptor: No hydrogen atom was selected (:LYS_at_HZ3),
ignoring...

 

PTRAJ: acceptor mask :SER_at_OG :SER_at_HG

Mask [:SER_at_OG] represents 0 atoms !!!NO ATOMS DETECTED!!!

Mask [:SER_at_HG] represents 1 atoms

WARNING in ptraj, acceptor: No heavy atom was selected (:SER_at_OG),
ignoring...

WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the

atom selection in the two masks :SER_at_OG and :SER_at_HG which contain 0 and 1

atoms respectively. Ignoring...

 

PTRAJ: acceptor mask :THR_at_OG1 :THR_at_HG1

Mask [:THR_at_OG1] represents 0 atoms !!!NO ATOMS DETECTED!!!

Mask [:THR_at_HG1] represents 0 atoms !!!NO ATOMS DETECTED!!!

WARNING in ptraj, acceptor: No heavy atom was selected (:THR_at_OG1),
ignoring...

WARNING in ptraj, acceptor: No hydrogen atom was selected (:THR_at_HG1),
ignoring...

 

PTRAJ: acceptor mask :ARG_at_NH2 :ARG_at_HH21

Mask [:ARG_at_NH2] represents 1 atoms

Mask [:ARG_at_HH21] represents 1 atoms

 

PTRAJ: acceptor mask :ARG_at_NH2 :ARG_at_HH22

Mask [:ARG_at_NH2] represents 1 atoms

Mask [:ARG_at_HH22] represents 1 atoms

 

PTRAJ: acceptor mask :ARG_at_NH1 :ARG_at_HH11

Mask [:ARG_at_NH1] represents 1 atoms

Mask [:ARG_at_HH11] represents 1 atoms

 

PTRAJ: acceptor mask :ARG_at_NH1 :ARG_at_HH12

Mask [:ARG_at_NH1] represents 1 atoms

Mask [:ARG_at_HH12] represents 1 atoms

 

PTRAJ: acceptor mask :ARG_at_NE :ARG_at_HE

Mask [:ARG_at_NE] represents 1 atoms

Mask [:ARG_at_HE] represents 1 atoms

 

PTRAJ: acceptor mask :HIS_at_NE2 :HIS_at_HE2

Mask [:HIS_at_NE2] represents 2 atoms

Mask [:HIS_at_HE2] represents 3 atoms

WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the

atom selection in the two masks :HIS_at_NE2 and :HIS_at_HE2 which contain 2 and 3

atoms respectively. Ignoring...

 

PTRAJ: acceptor mask :HIE_at_NE2 :HIE_at_HE2

Mask [:HIE_at_NE2] represents 2 atoms

Mask [:HIE_at_HE2] represents 2 atoms

 

PTRAJ: acceptor mask :HID_at_ND1 :HID_at_HD1

Mask [:HID_at_ND1] represents 2 atoms

Mask [:HID_at_HD1] represents 1 atoms

WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the

atom selection in the two masks :HID_at_ND1 and :HID_at_HD1 which contain 2 and 1

atoms respectively. Ignoring...

 

PTRAJ: acceptor mask :HIP_at_ND1,NE2 :HIP_at_HE2,HD1

Mask [:HIP_at_ND1,NE2] represents 4 atoms

Mask [:HIP_at_HE2,HD1] represents 4 atoms

 

PTRAJ: donor mask @O

Mask [@O] represents 8 atoms

 

PTRAJ: acceptor mask :2-8_at_N :2-8_at_H

Mask [:2-8_at_N] represents 7 atoms

Mask [:2-8_at_H] represents 7 atoms

 

PTRAJ: donor mask @OXT

Mask [@OXT] represents 1 atoms

 

PTRAJ: acceptor mask :1_at_N :1_at_H1

Mask [:1_at_N] represents 1 atoms

Mask [:1_at_H1] represents 1 atoms

 

PTRAJ: acceptor mask :1_at_N :1_at_H2

Mask [:1_at_N] represents 1 atoms

Mask [:1_at_H2] represents 1 atoms

 

PTRAJ: acceptor mask :1_at_N :1_at_H3

Mask [:1_at_N] represents 1 atoms

Mask [:1_at_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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