Hi All,
I have prepared prmtop and inpcrd files as discussed in a recent thread
(can't find the link in the archive yet).
But I am getting strange warnings from tleap that there are large bonds
between atoms of the same residues (protein and ligand).
I have checked the coordinates for a couple of them and this doesn't look
to be the case.
Can you please take a look and suggest me if these are due to bad pdb
structure or some other error?
Thanks a lot.
ukmcdwlx005 189% tleap -s -f leap.in
-I: Adding /apps/ambertools/amber12/rhel6-x64/dat/leap/prep to search path.
-I: Adding /apps/ambertools/amber12/rhel6-x64/dat/leap/lib to search path.
-I: Adding /apps/ambertools/amber12/rhel6-x64/dat/leap/parm to search path.
-I: Adding /apps/ambertools/amber12/rhel6-x64/dat/leap/cmd to search path.
-s: Ignoring startup file: leaprc
-f: Source leap.in.
Welcome to LEaP!
Sourcing: ./leap.in
----- Source: /apps/ambertools/amber12/rhel6-x64/dat/leap/cmd/leaprc.ff99SB
----- Source of
/apps/ambertools/amber12/rhel6-x64/dat/leap/cmd/leaprc.ff99SB done
Log file: ./leap.log
Loading parameters:
/apps/ambertools/amber12/rhel6-x64/dat/leap/parm/parm99.dat
Reading title:
PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
incl.02/04/99
Loading parameters:
/apps/ambertools/amber12/rhel6-x64/dat/leap/parm/frcmod.ff99SB
Reading force field modification type file (frcmod)
Reading title:
Modification/update of parm99.dat (Hornak & Simmerling)
Loading library:
/apps/ambertools/amber12/rhel6-x64/dat/leap/lib/all_nucleic94.lib
Loading library:
/apps/ambertools/amber12/rhel6-x64/dat/leap/lib/all_amino94.lib
Loading library:
/apps/ambertools/amber12/rhel6-x64/dat/leap/lib/all_aminoct94.lib
Loading library:
/apps/ambertools/amber12/rhel6-x64/dat/leap/lib/all_aminont94.lib
Loading library: /apps/ambertools/amber12/rhel6-x64/dat/leap/lib/ions94.lib
Loading library:
/apps/ambertools/amber12/rhel6-x64/dat/leap/lib/solvents.lib
----- Source: /apps/ambertools/amber12/rhel6-x64/dat/leap/cmd/leaprc.gaff
----- Source of /apps/ambertools/amber12/rhel6-x64/dat/leap/cmd/leaprc.gaff
done
Log file: ./leap.log
Loading parameters:
/apps/ambertools/amber12/rhel6-x64/dat/leap/parm/gaff.dat
Reading title:
AMBER General Force Field for organic molecules (Version 1.4, March 2010)
add. info. at the end
Loading Mol2 file: ./CYS_HS.mol2
Reading MOLECULE named CYP-IC6
UNIT name: CYP-IC6
Head atom: .R<CYP 1>.A<N 1>
Tail atom: .R<CYP 1>.A<C 9>
Contents:
R<CYP 1>
Loading Mol2 file: ./HEM_pentacoordinateHS.mol2
Reading MOLECULE named HEM-IC6
Loading parameters: ./HEM_HS.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
Loading Mol2 file: ./ERY.mol2
Reading MOLECULE named ERY
Loading parameters: ./ERY.frcmod
Reading force field modification type file (frcmod)
Reading title:
remark goes here
Loading PDB file: ./2J0D_prepared1.pdb
(starting new molecule for chain 1)
(starting new molecule for chain 2)
(starting new molecule for chain 3)
(starting new molecule for chain 4)
Added missing heavy atom: .R<CTYR 99>.A<OXT 22>
Added missing heavy atom: .R<CPRO 199>.A<OXT 15>
Added missing heavy atom: .R<CSER 299>.A<OXT 12>
Added missing heavy atom: .R<CTYR 399>.A<OXT 22>
Added missing heavy atom: .R<CARG 496>.A<OXT 25>
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-NB-FE-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-NA-FE-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-ND-FE-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
+Currently only Sp3-Sp3/Sp3-Sp2/Sp2-Sp2 are supported
+---Tried to superimpose torsions for: *-NC-FE-*
+--- With Sp2 - Sp0
+--- Sp0 probably means a new atom type is involved
+--- which needs to be added via addAtomTypes
total atoms in file: 3868
Leap added 3970 missing atoms according to residue templates:
5 Heavy
3965 H / lone pairs
Scaling up box by a factor of 1.252551 to meet diagonal cut criterion
Solute vdw bounding box: 77.194 75.259 55.253
Total bounding box for atom centers: 107.256 107.256 107.256
(box expansion for 'iso' is 28.0%)
Solvent unit box: 18.774 18.774 18.774
Volume: 634337.815 A^3 (oct)
Total mass 340597.068 amu, Density 0.892 g/cc
Added 15848 residues.
Total unperturbed charge: 3.005998
Total perturbed charge: 3.005998
3 Cl- ions required to neutralize.
Adding 3 counter ions to "P450" using 1A grid
Grid extends from solute vdw + 2.47 to 8.47
Resolution: 1.00 Angstrom.
grid build: 0 sec
Solvent present: replacing closest with ion
when steric overlaps occur
Calculating grid charges
charges: 16 sec
(Replacing solvent molecule)
Placed Cl- in P450 at (-14.72, -8.49, 1.48).
(Replacing solvent molecule)
Placed Cl- in P450 at (12.49, 10.65, -22.81).
(Replacing solvent molecule)
Placed Cl- in P450 at (-22.20, -7.90, 26.79).
Done adding ions.
> saveamberparam P450 P450_2J0D.prmtop P450_2J0D.inpcrd
ERROR: syntax error
> saveamberparm P450 P450_2J0D.prmtop P450_2J0D.inpcrd
Checking Unit.
WARNING: There is a bond of 20.901524 angstroms between:
------- .R<CYS 58>.A<CB 5> and .R<CYS 58>.A<SG 8>
WARNING: There is a bond of 20.837498 angstroms between:
------- .R<MET 59>.A<SD 11> and .R<MET 59>.A<CE 12>
WARNING: There is a bond of 18.891764 angstroms between:
------- .R<CTYR 99>.A<N 1> and .R<CTYR 99>.A<CA 3>
WARNING: There is a bond of 19.115078 angstroms between:
------- .R<NSER 100>.A<C 12> and .R<VAL 101>.A<N 1>
WARNING: There is a bond of 20.475057 angstroms between:
------- .R<NSER 100>.A<CB 7> and .R<NSER 100>.A<OG 10>
WARNING: There is a bond of 19.923242 angstroms between:
------- .R<THR 103>.A<N 1> and .R<THR 103>.A<CA 3>
WARNING: There is a bond of 19.727978 angstroms between:
------- .R<ASN 104>.A<CA 3> and .R<ASN 104>.A<C 13>
WARNING: There is a bond of 20.807121 angstroms between:
------- .R<ARG 105>.A<C 23> and .R<ARG 105>.A<O 24>
WARNING: There is a bond of 20.885143 angstroms between:
------- .R<ARG 106>.A<CA 3> and .R<ARG 106>.A<C 23>
WARNING: There is a bond of 18.744920 angstroms between:
------- .R<PHE 108>.A<CE2 15> and .R<PHE 108>.A<CD2 17>
WARNING: There is a bond of 19.774763 angstroms between:
------- .R<PHE 108>.A<CE1 11> and .R<PHE 108>.A<CZ 13>
WARNING: There is a bond of 19.775034 angstroms between:
------- .R<VAL 111>.A<C 15> and .R<GLY 112>.A<N 1>
WARNING: There is a bond of 19.894110 angstroms between:
------- .R<VAL 111>.A<CA 3> and .R<VAL 111>.A<C 15>
WARNING: There is a bond of 20.054649 angstroms between:
------- .R<GLY 112>.A<C 6> and .R<GLY 112>.A<O 7>
WARNING: There is a bond of 19.604853 angstroms between:
------- .R<GLY 112>.A<N 1> and .R<GLY 112>.A<CA 3>
WARNING: There is a bond of 20.685790 angstroms between:
------- .R<LYS 115>.A<C 21> and .R<SER 116>.A<N 1>
WARNING: There is a bond of 19.905225 angstroms between:
------- .R<LYS 115>.A<N 1> and .R<LYS 115>.A<CA 3>
WARNING: There is a bond of 19.541382 angstroms between:
------- .R<SER 119>.A<C 10> and .R<SER 119>.A<O 11>
WARNING: There is a bond of 21.170183 angstroms between:
------- .R<ILE 120>.A<CB 5> and .R<ILE 120>.A<CG1 11>
WARNING: There is a bond of 19.438126 angstroms between:
------- .R<ILE 120>.A<N 1> and .R<ILE 120>.A<CA 3>
WARNING: There is a bond of 20.260686 angstroms between:
------- .R<ARG 128>.A<CD 11> and .R<ARG 128>.A<NE 14>
WARNING: There is a bond of 19.588907 angstroms between:
------- .R<ARG 128>.A<CG 8> and .R<ARG 128>.A<CD 11>
WARNING: There is a bond of 18.918132 angstroms between:
------- .R<ARG 128>.A<CB 5> and .R<ARG 128>.A<CG 8>
WARNING: There is a bond of 20.067992 angstroms between:
------- .R<ARG 128>.A<CA 3> and .R<ARG 128>.A<C 23>
WARNING: There is a bond of 20.398286 angstroms between:
------- .R<ARG 130>.A<NE 14> and .R<ARG 130>.A<CZ 16>
WARNING: There is a bond of 20.032240 angstroms between:
------- .R<PHE 137>.A<C 19> and .R<THR 138>.A<N 1>
WARNING: There is a bond of 18.979897 angstroms between:
------- .R<PHE 137>.A<CE1 11> and .R<PHE 137>.A<CZ 13>
WARNING: There is a bond of 19.799136 angstroms between:
------- .R<PHE 137>.A<CG 8> and .R<PHE 137>.A<CD1 9>
WARNING: There is a bond of 19.707132 angstroms between:
------- .R<PHE 137>.A<CA 3> and .R<PHE 137>.A<C 19>
WARNING: There is a bond of 20.042140 angstroms between:
------- .R<THR 138>.A<CA 3> and .R<THR 138>.A<CB 5>
WARNING: There is a bond of 20.227088 angstroms between:
------- .R<THR 138>.A<N 1> and .R<THR 138>.A<CA 3>
WARNING: There is a bond of 19.732610 angstroms between:
------- .R<GLY 140>.A<C 6> and .R<LYS 141>.A<N 1>
WARNING: There is a bond of 20.251158 angstroms between:
------- .R<LYS 141>.A<C 21> and .R<LEU 142>.A<N 1>
WARNING: There is a bond of 19.821723 angstroms between:
------- .R<GLU 144>.A<C 14> and .R<MET 145>.A<N 1>
WARNING: There is a bond of 20.209895 angstroms between:
------- .R<GLU 144>.A<N 1> and .R<GLU 144>.A<CA 3>
WARNING: There is a bond of 19.333100 angstroms between:
------- .R<MET 145>.A<CB 5> and .R<MET 145>.A<CG 8>
WARNING: There is a bond of 20.073760 angstroms between:
------- .R<ILE 148>.A<CA 3> and .R<ILE 148>.A<CB 5>
WARNING: There is a bond of 19.781674 angstroms between:
------- .R<TYR 152>.A<CZ 13> and .R<TYR 152>.A<OH 14>
WARNING: There is a bond of 19.835748 angstroms between:
------- .R<ILE 184>.A<CA 3> and .R<ILE 184>.A<C 18>
WARNING: There is a bond of 19.502835 angstroms between:
------- .R<ILE 193>.A<C 18> and .R<ILE 193>.A<O 19>
WARNING: There is a bond of 20.676382 angstroms between:
------- .R<ASP 194>.A<N 1> and .R<ASP 194>.A<CA 3>
WARNING: There is a bond of 20.836815 angstroms between:
------- .R<ASN 198>.A<C 13> and .R<CPRO 199>.A<N 1>
WARNING: There is a bond of 19.207179 angstroms between:
------- .R<NGLN 200>.A<CA 5> and .R<NGLN 200>.A<CB 7>
WARNING: There is a bond of 19.750778 angstroms between:
------- .R<LYS 208>.A<CB 5> and .R<LYS 208>.A<CG 8>
WARNING: There is a bond of 20.549701 angstroms between:
------- .R<LEU 211>.A<CA 3> and .R<LEU 211>.A<CB 5>
WARNING: There is a bond of 20.359004 angstroms between:
------- .R<LEU 211>.A<CA 3> and .R<LEU 211>.A<C 18>
WARNING: There is a bond of 21.048016 angstroms between:
------- .R<ARG 212>.A<CA 3> and .R<ARG 212>.A<C 23>
WARNING: There is a bond of 18.933685 angstroms between:
------- .R<ASP 214>.A<CA 3> and .R<ASP 214>.A<CB 5>
WARNING: There is a bond of 20.530980 angstroms between:
------- .R<PHE 215>.A<C 19> and .R<LEU 216>.A<N 1>
WARNING: There is a bond of 20.628045 angstroms between:
------- .R<PHE 219>.A<C 19> and .R<PHE 220>.A<N 1>
WARNING: There is a bond of 20.406414 angstroms between:
------- .R<PHE 219>.A<CE2 15> and .R<PHE 219>.A<CD2 17>
WARNING: There is a bond of 19.251968 angstroms between:
------- .R<PHE 219>.A<CE1 11> and .R<PHE 219>.A<CZ 13>
WARNING: There is a bond of 20.229592 angstroms between:
------- .R<PHE 219>.A<CA 3> and .R<PHE 219>.A<CB 5>
WARNING: There is a bond of 28.335125 angstroms between:
------- .R<PHE 220>.A<CE2 15> and .R<PHE 220>.A<CD2 17>
WARNING: There is a bond of 27.975862 angstroms between:
------- .R<PHE 220>.A<CD1 9> and .R<PHE 220>.A<CE1 11>
WARNING: There is a bond of 20.132399 angstroms between:
------- .R<SER 222>.A<C 10> and .R<SER 222>.A<O 11>
WARNING: There is a bond of 20.146228 angstroms between:
------- .R<SER 222>.A<C 10> and .R<ILE 223>.A<N 1>
WARNING: There is a bond of 20.143205 angstroms between:
------- .R<SER 222>.A<CB 5> and .R<SER 222>.A<OG 8>
WARNING: There is a bond of 20.722135 angstroms between:
------- .R<SER 222>.A<CA 3> and .R<SER 222>.A<CB 5>
WARNING: There is a bond of 20.005051 angstroms between:
------- .R<ILE 223>.A<C 18> and .R<ILE 223>.A<O 19>
WARNING: There is a bond of 19.554786 angstroms between:
------- .R<ILE 223>.A<CA 3> and .R<ILE 223>.A<C 18>
WARNING: There is a bond of 20.933268 angstroms between:
------- .R<VAL 225>.A<C 15> and .R<PHE 226>.A<N 1>
WARNING: There is a bond of 19.450270 angstroms between:
------- .R<ASN 237>.A<C 13> and .R<ASN 237>.A<O 14>
WARNING: There is a bond of 19.893495 angstroms between:
------- .R<ILE 238>.A<C 18> and .R<CYS 239>.A<N 1>
WARNING: There is a bond of 19.211867 angstroms between:
------- .R<HIE 287>.A<C 16> and .R<HIE 287>.A<O 17>
WARNING: There is a bond of 18.871768 angstroms between:
------- .R<HIE 287>.A<CA 3> and .R<HIE 287>.A<CB 5>
WARNING: There is a bond of 21.176645 angstroms between:
------- .R<LYS 288>.A<CB 5> and .R<LYS 288>.A<CG 8>
WARNING: There is a bond of 19.439746 angstroms between:
------- .R<PHE 302>.A<C 19> and .R<PHE 302>.A<O 20>
WARNING: There is a bond of 19.851588 angstroms between:
------- .R<ILE 303>.A<C 18> and .R<PHE 304>.A<N 1>
WARNING: There is a bond of 19.243497 angstroms between:
------- .R<ILE 303>.A<CA 3> and .R<ILE 303>.A<C 18>
WARNING: There is a bond of 20.270792 angstroms between:
------- .R<PHE 304>.A<CA 3> and .R<PHE 304>.A<CB 5>
WARNING: There is a bond of 20.282716 angstroms between:
------- .R<PHE 304>.A<N 1> and .R<PHE 304>.A<CA 3>
WARNING: There is a bond of 19.402320 angstroms between:
------- .R<MET 371>.A<CA 3> and .R<MET 371>.A<C 16>
WARNING: There is a bond of 19.343980 angstroms between:
------- .R<LYS 378>.A<N 1> and .R<LYS 378>.A<CA 3>
WARNING: There is a bond of 21.078747 angstroms between:
------- .R<LYS 379>.A<CA 3> and .R<LYS 379>.A<C 21>
WARNING: There is a bond of 20.057094 angstroms between:
------- .R<LYS 390>.A<CB 5> and .R<LYS 390>.A<CG 8>
WARNING: There is a bond of 19.535055 angstroms between:
------- .R<CTYR 399>.A<CE2 16> and .R<CTYR 399>.A<CD2 18>
WARNING: There is a bond of 19.705675 angstroms between:
------- .R<CTYR 399>.A<CG 8> and .R<CTYR 399>.A<CD2 18>
WARNING: There is a bond of 19.856401 angstroms between:
------- .R<CTYR 399>.A<CB 5> and .R<CTYR 399>.A<CG 8>
WARNING: There is a bond of 19.249097 angstroms between:
------- .R<HIE 402>.A<C 16> and .R<ARG 403>.A<N 1>
WARNING: There is a bond of 20.901105 angstroms between:
------- .R<HIE 402>.A<CA 3> and .R<HIE 402>.A<CB 5>
WARNING: There is a bond of 19.987579 angstroms between:
------- .R<HIE 402>.A<CA 3> and .R<HIE 402>.A<C 16>
WARNING: There is a bond of 20.405535 angstroms between:
------- .R<ARG 403>.A<CB 5> and .R<ARG 403>.A<CG 8>
WARNING: There is a bond of 20.131809 angstroms between:
------- .R<TRP 408>.A<C 23> and .R<THR 409>.A<N 1>
WARNING: There is a bond of 19.748906 angstroms between:
------- .R<TRP 408>.A<NE1 11> and .R<TRP 408>.A<CE2 13>
WARNING: There is a bond of 19.386414 angstroms between:
------- .R<TRP 408>.A<CG 8> and .R<TRP 408>.A<CD1 9>
WARNING: There is a bond of 20.115849 angstroms between:
------- .R<TRP 408>.A<CA 3> and .R<TRP 408>.A<CB 5>
WARNING: There is a bond of 20.991188 angstroms between:
------- .R<THR 409>.A<CB 5> and .R<THR 409>.A<CG2 7>
WARNING: There is a bond of 19.982748 angstroms between:
------- .R<PRO 411>.A<CG 5> and .R<PRO 411>.A<CB 8>
WARNING: There is a bond of 19.806896 angstroms between:
------- .R<PRO 411>.A<CD 2> and .R<PRO 411>.A<CG 5>
WARNING: There is a bond of 19.020003 angstroms between:
------- .R<ASN 426>.A<C 13> and .R<ASN 426>.A<O 14>
WARNING: There is a bond of 21.022285 angstroms between:
------- .R<ASN 426>.A<CB 5> and .R<ASN 426>.A<CG 8>
WARNING: There is a bond of 20.246243 angstroms between:
------- .R<ASN 426>.A<CA 3> and .R<ASN 426>.A<CB 5>
WARNING: There is a bond of 18.935037 angstroms between:
------- .R<ILE 427>.A<C 18> and .R<ASP 428>.A<N 1>
WARNING: There is a bond of 19.945490 angstroms between:
------- .R<TYR 432>.A<N 1> and .R<TYR 432>.A<CA 3>
WARNING: There is a bond of 20.154212 angstroms between:
------- .R<THR 433>.A<CA 3> and .R<THR 433>.A<CB 5>
WARNING: There is a bond of 19.380348 angstroms between:
------- .R<GLY 436>.A<C 6> and .R<SER 437>.A<N 1>
WARNING: There is a bond of 19.640287 angstroms between:
------- .R<ARG 440>.A<C 23> and .R<ASN 441>.A<N 1>
WARNING: There is a bond of 19.564918 angstroms between:
------- .R<ARG 440>.A<CD 11> and .R<ARG 440>.A<NE 14>
WARNING: There is a bond of 20.641507 angstroms between:
------- .R<ILE 443>.A<CB 5> and .R<ILE 443>.A<CG1 11>
WARNING: There is a bond of 20.727355 angstroms between:
------- .R<HEM 497>.A<CBD 65> and .R<HEM 497>.A<CGD 68>
WARNING: There is a bond of 20.299434 angstroms between:
------- .R<HEM 497>.A<CBA 62> and .R<HEM 497>.A<CGA 69>
WARNING: There is a bond of 20.402226 angstroms between:
------- .R<HEM 497>.A<C2D 12> and .R<HEM 497>.A<CMD 48>
WARNING: There is a bond of 20.016604 angstroms between:
------- .R<ERY 498>.A<C9 13> and .R<ERY 498>.A<O11 14>
WARNING: There is a bond of 19.819553 angstroms between:
------- .R<ERY 498>.A<C8 12> and .R<ERY 498>.A<C33 20>
WARNING: There is a bond of 19.311291 angstroms between:
------- .R<ERY 498>.A<C3 7> and .R<ERY 498>.A<O3 17>
WARNING: There is a bond of 20.035048 angstroms between:
------- .R<ERY 498>.A<C2 6> and .R<ERY 498>.A<C30 25>
-- ignoring the warnings.
Building topology.
Building atom parameters.
Building bond parameters.
Building angle parameters.
Building proper torsion parameters.
Building improper torsion parameters.
total 1470 improper torsions applied
Building H-Bond parameters.
Not Marking per-residue atom chain types.
Marking per-residue atom chain types.
(Residues lacking connect0/connect1 -
these don't have chain types marked:
res total affected
ACE 1
CARG 1
CPRO 1
CSER 1
CTYR 2
CYP 1
ERY 1
HEM 1
NALA 1
NGLN 1
NILE 1
NSER 1
WAT 15845
)
(no restraints)
>
--
With Regards.
Dr. Vaibhav A. Dixit,
Postdoctoral Research Scientist,
Etherow F40/6,
AstraZeneca,
Charter Way,
Silk Road Business Park,
Macclesfield,
Cheshire,
England,
SK10 2NX
Ext. No. 20278
Email: Vaibhav.Dixit.astrazeneca.com
Moblie Number: +44-7448233157, +91-7709129400.
http://scholar.google.co.in/citations?user=X876BKcAAAAJ&hl=en&oi=sra
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Received on Thu Apr 09 2015 - 04:30:05 PDT
