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.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 :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.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
> 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.OE1
Mask [:GLN.OE1] represents 14 atoms
PTRAJ: donor mask :GLN.NE2
Mask [:GLN.NE2] represents 14 atoms
PTRAJ: donor mask :ASN.OD1
Mask [:ASN.OD1] represents 11 atoms
PTRAJ: donor mask :ASN.ND2
Mask [:ASN.ND2] represents 11 atoms
PTRAJ: donor mask :TYR.OH
Mask [:TYR.OH] represents 7 atoms
PTRAJ: donor mask :ASP.OD1
Mask [:ASP.OD1] represents 11 atoms
PTRAJ: donor mask :ASP.OD2
Mask [:ASP.OD2] represents 11 atoms
PTRAJ: donor mask :GLU.OE1
Mask [:GLU.OE1] represents 12 atoms
PTRAJ: donor mask :GLU.OE2
Mask [:GLU.OE2] represents 12 atoms
PTRAJ: donor mask :SER.OG
Mask [:SER.OG] represents 17 atoms
PTRAJ: donor mask :THR.OG1
Mask [:THR.OG1] represents 6 atoms
PTRAJ: donor mask :HIS.ND1
Mask [:HIS.ND1] represents 8 atoms
PTRAJ: donor mask :HIE.ND1
Mask [:HIE.ND1] represents 8 atoms
PTRAJ: donor mask :HID.NE2
Mask [:HID.NE2] represents 22 atoms
PTRAJ: acceptor mask :ASN.ND2 :ASN.HD21
Mask [:ASN.ND2] represents 11 atoms
Mask [:ASN.HD21] represents 11 atoms
PTRAJ: acceptor mask :ASN.ND2 :ASN.HD22
Mask [:ASN.ND2] represents 11 atoms
Mask [:ASN.HD22] represents 11 atoms
PTRAJ: acceptor mask :TYR.OH :TYR.HH
Mask [:TYR.OH] represents 7 atoms
Mask [:TYR.HH] represents 7 atoms
PTRAJ: acceptor mask :GLN.NE2 :GLN.HE21
Mask [:GLN.NE2] represents 14 atoms
Mask [:GLN.HE21] represents 14 atoms
PTRAJ: acceptor mask :GLN.NE2 :GLN.HE22
Mask [:GLN.NE2] represents 14 atoms
Mask [:GLN.HE22] represents 14 atoms
PTRAJ: acceptor mask :TRP.NE1 :TRP.HE1
Mask [:TRP.NE1] represents 4 atoms
Mask [:TRP.HE1] represents 4 atoms
PTRAJ: acceptor mask :LYS.NZ :LYS.HZ1
Mask [:LYS.NZ] represents 14 atoms
Mask [:LYS.HZ1] represents 14 atoms
PTRAJ: acceptor mask :LYS.NZ :LYS.HZ2
Mask [:LYS.NZ] represents 14 atoms
Mask [:LYS.HZ2] represents 14 atoms
PTRAJ: acceptor mask :LYS.NZ :LYS.HZ3
Mask [:LYS.NZ] represents 14 atoms
Mask [:LYS.HZ3] represents 14 atoms
PTRAJ: acceptor mask :SER.OG :SER.HG
Mask [:SER.OG] represents 17 atoms
Mask [:SER.HG] represents 17 atoms
PTRAJ: acceptor mask :THR.OG1 :THR.HG1
Mask [:THR.OG1] represents 6 atoms
Mask [:THR.HG1] represents 6 atoms
PTRAJ: acceptor mask :ARG.NH2 :ARG.HH21
Mask [:ARG.NH2] represents 14 atoms
Mask [:ARG.HH21] represents 14 atoms
PTRAJ: acceptor mask :ARG.NH2 :ARG.HH22
Mask [:ARG.NH2] represents 14 atoms
Mask [:ARG.HH22] represents 14 atoms
PTRAJ: acceptor mask :ARG.NH1 :ARG.HH11
Mask [:ARG.NH1] represents 14 atoms
Mask [:ARG.HH11] represents 14 atoms
PTRAJ: acceptor mask :ARG.NH1 :ARG.HH12
Mask [:ARG.NH1] represents 14 atoms
Mask [:ARG.HH12] represents 14 atoms
PTRAJ: acceptor mask :ARG.NE :ARG.HE
Mask [:ARG.NE] represents 14 atoms
Mask [:ARG.HE] represents 14 atoms
PTRAJ: acceptor mask :HIS.NE2 :HIS.HE2
Mask [:HIS.NE2] represents 22 atoms
Mask [:HIS.HE2] represents 59 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 22
and 59
atoms respectively. Ignoring...
PTRAJ: acceptor mask :HIE.NE2 :HIE.HE2
Mask [:HIE.NE2] represents 8 atoms
Mask [:HIE.HE2] represents 8 atoms
PTRAJ: acceptor mask :HID.ND1 :HID.HD1
Mask [:HID.ND1] represents 8 atoms
Mask [:HID.HD1] represents 28 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 8 and 28
atoms respectively. Ignoring...
PTRAJ: acceptor mask :HIP.ND1,NE2 :HIP.HE2,HD1
Mask [:HIP.ND1,NE2] represents 30 atoms
Mask [:HIP.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.ND1,NE2 and :HIP.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.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
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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Received on Wed Jul 05 2006 - 06:07:14 PDT
