AMBER Archive (2006)

Subject: AMBER: hbond analysis

From: Claire Zerafa (cporteli_at_waldonet.net.mt)
Date: Mon Jul 03 2006 - 16:06:22 CDT

Dear amber users

I am running hbond analysis on a nuclear receptor steroid complex. My
input file is as follows:

> trajin
> /DATA/CORTICOSTERONE_DYNAMICS/1e3g_corticosterone_docked_md2.mdcrd.gz
> trajin
> /DATA/CORTICOSTERONE_DYNAMICS/1e3g_corticosterone_docked_md3.mdcrd.gz
> trajin
> /DATA/CORTICOSTERONE_DYNAMICS/1e3g_corticosterone_docked_md4.mdcrd.gz
> trajin
> /DATA/CORTICOSTERONE_DYNAMICS/1e3g_corticosterone_docked_md5.mdrcd.gz
> trajin
> /DATA/CORTICOSTERONE_DYNAMICS/1e3g_corticosterone_docked_md6.mdrcd.gz
> trajin
> /DATA/CORTICOSTERONE_DYNAMICS/1e3g_corticosterone_docked_md7.mdcrd.gz
> trajin
> /DATA/CORTICOSTERONE_DYNAMICS/1e3g_corticosterone_docked_md8.mdcrd.gz
> trajin
> /DATA/CORTICOSTERONE_DYNAMICS/1e3g_corticosterone_docked_md9.mdcrd.gz
> trajin
> /DATA/CORTICOSTERONE_DYNAMICS/1e3g_corticosterone_docked_md10.mdcrd.gz
>
> #-- 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 :UNK @O50
> donor mask :UNK @O24
> donor mask :UNK @O11,H12
> donor mask :UNK @O26,H27
>
> acceptor mask :UNK @O11,H12
> acceptor mask :UNK @O26,H27
>
> #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
> go

I think there is something wrong with my OH nomenclature for the ligand
donor and acceptor sites. They total to 0 atoms as may be seen in the
output file below. Also, the process bombs out as may also be seen. Is
this a memory problem? The files are correctly designated, and the
co-ordinate files are correctly read at the beginning of the process and
an alert that says out of logical swap space during fork/sproc comes
up. Is there anything I can do to solve this?

Thanks
claire

Amber8 Module: ptraj

 CYX GLN PRO ILE PHE LEU ASN VAL LEU GLU
 ALA ILE GLU PRO GLY VAL VAL CYS ALA GLY
 HIE ASP ASN ASN GLN PRO ASP SER PHE ALA
 ALA LEU LEU SER SER LEU ASN GLU LEU GLY
 GLU ARG GLN LEU VAL HIE VAL VAL LYS TRP
 ALA LYS ALA LEU PRO GLY PHE ARG ASN LEU
 HIE VAL ASP ASP GLN MET ALA VAL ILE GLN
 TYR SER TRP MET GLY LEU MET VAL PHE ALA
 MET GLY TRP ARG SER PHE THR ASN VAL ASN
 SER ARG MET LEU TYR PHE ALA PRO ASP LEU
 VAL PHE ASN GLU TYR ARG MET HIE LYS SER
 ARG MET TYR SER GLN CYS VAL ARG MET ARG
 HIE LEU SER GLN GLU PHE GLY TRP LEU GLN
 ILE THR PRO GLN GLU PHE LEU CYS MET LYS
 ALA LEU LEU LEU PHE SER ILE ILE PRO VAL
 ASP GLY LEU LYS ASN GLN LYS PHE PHE ASP
 GLU LEU ARG MET ASN TYR ILE LYS GLU LEU
 ASP ARG ILE ILE ALA CYX LYS ARG LYS ASN
 PRO THR SER CYS SER ARG ARG PHE TYR GLN
 LEU THR LYS LEU LEU ASP SER VAL GLN PRO
 ILE ALA ARG GLU LEU HIE GLN PHE THR PHE
 ASP LEU LEU ILE LYS SER HIE MET VAL SER
 VAL ASP PHE PRO GLU MET MET ALA GLU ILE
 ILE SER VAL GLN VAL PRO LYS ILE LEU SER
 GLY LYS VAL LYS PRO ILE TYR PHE HIE THR
 UNK WAT WAT WAT WAT WAT WAT WAT WAT WAT
 WAT WAT WAT WAT WAT WAT WAT WAT WAT WAT
 ...
 WAT
Scanning Box
Successfully completed readParm.

PTRAJ: Processing input file...
       Input is from standard input

PTRAJ: trajin
/DATA/CORTICOSTERONE_DYNAMICS/1e3g_corticosterone_docked_md2.mdcrd.gz

PTRAJ: trajin
/DATA/CORTICOSTERONE_DYNAMICS/1e3g_corticosterone_docked_md3.mdcrd.gz

PTRAJ: trajin
/DATA/CORTICOSTERONE_DYNAMICS/1e3g_corticosterone_docked_md4.mdcrd.gz

PTRAJ: trajin
/DATA/CORTICOSTERONE_DYNAMICS/1e3g_corticosterone_docked_md5.mdrcd.gz

PTRAJ: trajin
/DATA/CORTICOSTERONE_DYNAMICS/1e3g_corticosterone_docked_md6.mdrcd.gz

PTRAJ: trajin
/DATA/CORTICOSTERONE_DYNAMICS/1e3g_corticosterone_docked_md7.mdcrd.gz

PTRAJ: trajin
/DATA/CORTICOSTERONE_DYNAMICS/1e3g_corticosterone_docked_md8.mdcrd.gz

PTRAJ: trajin
/DATA/CORTICOSTERONE_DYNAMICS/1e3g_corticosterone_docked_md9.mdcrd.gz

PTRAJ: trajin
/DATA/CORTICOSTERONE_DYNAMICS/1e3g_corticosterone_docked_md10.mdcrd.gz

PTRAJ: donor mask :GLN_at_OE1
Mask [:GLN_at_OE1] represents 14 atoms

PTRAJ: donor mask :GLN_at_NE2
Mask [:GLN_at_NE2] represents 14 atoms

PTRAJ: donor mask :ASN_at_OD1
Mask [:ASN_at_OD1] represents 11 atoms

PTRAJ: donor mask :ASN_at_ND2
Mask [:ASN_at_ND2] represents 11 atoms

PTRAJ: donor mask :TYR_at_OH
Mask [:TYR_at_OH] represents 7 atoms

PTRAJ: donor mask :ASP_at_OD1
Mask [:ASP_at_OD1] represents 11 atoms

PTRAJ: donor mask :ASP_at_OD2
Mask [:ASP_at_OD2] represents 11 atoms

PTRAJ: donor mask :GLU_at_OE1
Mask [:GLU_at_OE1] represents 12 atoms

PTRAJ: donor mask :GLU_at_OE2
Mask [:GLU_at_OE2] represents 12 atoms

PTRAJ: donor mask :SER_at_OG
Mask [:SER_at_OG] represents 17 atoms

PTRAJ: donor mask :THR_at_OG1
Mask [:THR_at_OG1] represents 6 atoms

PTRAJ: donor mask :HIS_at_ND1
Mask [:HIS_at_ND1] represents 8 atoms

PTRAJ: donor mask :HIE_at_ND1
Mask [:HIE_at_ND1] represents 8 atoms

PTRAJ: donor mask :HID_at_NE2
Mask [:HID_at_NE2] represents 22 atoms

PTRAJ: acceptor mask :ASN_at_ND2 :ASN_at_HD21
Mask [:ASN_at_ND2] represents 11 atoms
Mask [:ASN_at_HD21] represents 11 atoms

PTRAJ: acceptor mask :ASN_at_ND2 :ASN_at_HD22
Mask [:ASN_at_ND2] represents 11 atoms
Mask [:ASN_at_HD22] represents 11 atoms

PTRAJ: acceptor mask :TYR_at_OH :TYR_at_HH
Mask [:TYR_at_OH] represents 7 atoms
Mask [:TYR_at_HH] represents 7 atoms

PTRAJ: acceptor mask :GLN_at_NE2 :GLN_at_HE21
Mask [:GLN_at_NE2] represents 14 atoms
Mask [:GLN_at_HE21] represents 14 atoms

PTRAJ: acceptor mask :GLN_at_NE2 :GLN_at_HE22
Mask [:GLN_at_NE2] represents 14 atoms
Mask [:GLN_at_HE22] represents 14 atoms

PTRAJ: acceptor mask :TRP_at_NE1 :TRP_at_HE1
Mask [:TRP_at_NE1] represents 4 atoms
Mask [:TRP_at_HE1] represents 4 atoms

PTRAJ: acceptor mask :LYS_at_NZ :LYS_at_HZ1
Mask [:LYS_at_NZ] represents 14 atoms
Mask [:LYS_at_HZ1] represents 14 atoms

PTRAJ: acceptor mask :LYS_at_NZ :LYS_at_HZ2
Mask [:LYS_at_NZ] represents 14 atoms
Mask [:LYS_at_HZ2] represents 14 atoms

PTRAJ: acceptor mask :LYS_at_NZ :LYS_at_HZ3
Mask [:LYS_at_NZ] represents 14 atoms
Mask [:LYS_at_HZ3] represents 14 atoms

PTRAJ: acceptor mask :SER_at_OG :SER_at_HG
Mask [:SER_at_OG] represents 17 atoms
Mask [:SER_at_HG] represents 17 atoms

PTRAJ: acceptor mask :THR_at_OG1 :THR_at_HG1
Mask [:THR_at_OG1] represents 6 atoms
Mask [:THR_at_HG1] represents 6 atoms

PTRAJ: acceptor mask :ARG_at_NH2 :ARG_at_HH21
Mask [:ARG_at_NH2] represents 14 atoms
Mask [:ARG_at_HH21] represents 14 atoms

PTRAJ: acceptor mask :ARG_at_NH2 :ARG_at_HH22
Mask [:ARG_at_NH2] represents 14 atoms
Mask [:ARG_at_HH22] represents 14 atoms

PTRAJ: acceptor mask :ARG_at_NH1 :ARG_at_HH11
Mask [:ARG_at_NH1] represents 14 atoms
Mask [:ARG_at_HH11] represents 14 atoms

PTRAJ: acceptor mask :ARG_at_NH1 :ARG_at_HH12
Mask [:ARG_at_NH1] represents 14 atoms
Mask [:ARG_at_HH12] represents 14 atoms

PTRAJ: acceptor mask :ARG_at_NE :ARG_at_HE
Mask [:ARG_at_NE] represents 14 atoms
Mask [:ARG_at_HE] represents 14 atoms

PTRAJ: acceptor mask :HIS_at_NE2 :HIS_at_HE2
Mask [:HIS_at_NE2] represents 22 atoms
Mask [:HIS_at_HE2] represents 59 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 22
and 59
atoms respectively. Ignoring...

PTRAJ: acceptor mask :HIE_at_NE2 :HIE_at_HE2
Mask [:HIE_at_NE2] represents 8 atoms
Mask [:HIE_at_HE2] represents 8 atoms

PTRAJ: acceptor mask :HID_at_ND1 :HID_at_HD1
Mask [:HID_at_ND1] represents 8 atoms
Mask [:HID_at_HD1] represents 28 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 8 and 28
atoms respectively. Ignoring...

PTRAJ: acceptor mask :HIP_at_ND1,NE2 :HIP_at_HE2,HD1
Mask [:HIP_at_ND1,NE2] represents 30 atoms
Mask [:HIP_at_HE2,HD1] represents 87 atoms
WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
atom selection in the two masks :HIP_at_ND1,NE2 and :HIP_at_HE2,HD1 which
contain 30 and 87
atoms respectively. Ignoring...

PTRAJ: donor mask :UNK @O50
Mask [:UNK] represents 55 atoms

PTRAJ: donor mask :UNK @O24
Mask [:UNK] represents 55 atoms

PTRAJ: donor mask :UNK @O11,H12
Mask [:UNK] represents 55 atoms

PTRAJ: donor mask :UNK @O26,H27
Mask [:UNK] represents 55 atoms

PTRAJ: acceptor mask :UNK @O11,H12
Mask [:UNK] represents 55 atoms
Mask [@O11,H12] represents 1 atoms
WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
atom selection in the two masks :UNK and @O11,H12 which contain 55 and 1
atoms respectively. Ignoring...

PTRAJ: acceptor mask :UNK @O26,H27
Mask [:UNK] represents 55 atoms
Mask [@O26,H27] represents 0 atoms !!!NO ATOMS DETECTED!!!
WARNING in ptraj, acceptor: No hydrogen atom was selected (@O26,H27),
ignoring...
WARNING in ptraj, acceptor: There is not a 1-1 correspondence between the
atom selection in the two masks :UNK and @O26,H27 which contain 55 and 0
atoms respectively. Ignoring...

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
FYI: No output trajectory specified (trajout), none will be saved.

PTRAJ: Successfully read the input file.
       Coordinate processing will occur on 3600 frames.
       Summary of I/O and actions follows:

INPUT COORDINATE FILES
  File
(/DATA/CORTICOSTERONE_DYNAMICS/1e3g_corticosterone_docked_md2.mdcrd.gz)
is an AMBER trajectory (with box info) with 400 sets
  File
(/DATA/CORTICOSTERONE_DYNAMICS/1e3g_corticosterone_docked_md3.mdcrd.gz)
is an AMBER trajectory (with box info) with 400 sets
  File
(/DATA/CORTICOSTERONE_DYNAMICS/1e3g_corticosterone_docked_md4.mdcrd.gz)
is an AMBER trajectory (with box info) with 400 sets
  File
(/DATA/CORTICOSTERONE_DYNAMICS/1e3g_corticosterone_docked_md5.mdrcd.gz)
is an AMBER trajectory (with box info) with 400 sets
  File
(/DATA/CORTICOSTERONE_DYNAMICS/1e3g_corticosterone_docked_md6.mdrcd.gz)
is an AMBER trajectory (with box info) with 400 sets
  File
(/DATA/CORTICOSTERONE_DYNAMICS/1e3g_corticosterone_docked_md7.mdcrd.gz)
is an AMBER trajectory (with box info) with 400 sets
  File
(/DATA/CORTICOSTERONE_DYNAMICS/1e3g_corticosterone_docked_md8.mdcrd.gz)
is an AMBER trajectory (with box info) with 400 sets
  File
(/DATA/CORTICOSTERONE_DYNAMICS/1e3g_corticosterone_docked_md9.mdcrd.gz)
is an AMBER trajectory (with box info) with 400 sets
  File
(/DATA/CORTICOSTERONE_DYNAMICS/1e3g_corticosterone_docked_md10.mdcrd.gz)
is an AMBER trajectory (with box info) with 400 sets

OUTPUT COORDINATE FILE
  NULL entry

ACTIONS
  1> HBOND saved to series hbt,
      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: 1690.06 MB
      donors: 198 acceptors: 207

Processing AMBER trajectory file
/DATA/CORTICOSTERONE_DYNAMICS/1e3g_corticosterone_docked_md2.mdcrd.gz

Set 1 .................................................
Set 50 .................................................
Set 100 .................................................
Set 150 .................................................
Set 200 .................................................
Set 250 .................................................
Set 300 .................................................
Set 350 .................................................
Set 400 WARNING in ptrajPreprocessInputCoordinates(): Error on opening
input coordinate file
(/DATA/CORTICOSTERONE_DYNAMICS/1e3g_corticosterone_docked_md3.mdcrd.gz)

>
>

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