On Thu, 2014-08-21 at 21:52 +0800, 闫玉娜 wrote:
> Hi all,
>
> I download a pdb named 1U13. It has the 'heme' cofactor. I have downloaded
> its parameters from ' http://www.pharmacy.manchester.ac.uk/bryce/amber'.
> But when I use it ,it gives the following errors:
>
>
> -I: Adding /home/yanyuna/Programs/amber11/dat/leap/prep to search path.
> -I: Adding /home/yanyuna/Programs/amber11/dat/leap/lib to search path.
> -I: Adding /home/yanyuna/Programs/amber11/dat/leap/parm to search path.
> -I: Adding /home/yanyuna/Programs/amber11/dat/leap/cmd to search path.
>
> Welcome to LEaP!
> (no leaprc in search path)
> > source leaprc.ff99SB
> ----- Source: /home/yanyuna/Programs/amber11/dat/leap/cmd/leaprc.ff99SB
> ----- Source of /home/yanyuna/Programs/amber11/dat/leap/cmd/leaprc.ff99SB
> done
> Log file: ./leap.log
> Loading parameters: /home/yanyuna/Programs/amber11/dat/leap/parm/parm99.dat
> Reading title:
> PARM99 for DNA,RNA,AA, organic molecules, TIP3P wat. Polariz.& LP
> incl.02/04/99
> Loading parameters:
> /home/yanyuna/Programs/amber11/dat/leap/parm/frcmod.ff99SB
> Reading force field modification type file (frcmod)
> Reading title:
> Modification/update of parm99.dat (Hornak & Simmerling)
> Loading library:
> /home/yanyuna/Programs/amber11/dat/leap/lib/all_nucleic94.lib
> Loading library: /home/yanyuna/Programs/amber11/dat/leap/lib/all_amino94.lib
> Loading library:
> /home/yanyuna/Programs/amber11/dat/leap/lib/all_aminoct94.lib
> Loading library:
> /home/yanyuna/Programs/amber11/dat/leap/lib/all_aminont94.lib
> Loading library: /home/yanyuna/Programs/amber11/dat/leap/lib/ions94.lib
> Loading library: /home/yanyuna/Programs/amber11/dat/leap/lib/solvents.lib
> > loadamberparams hem.frcmod
> Loading parameters: ./hem.frcmod
> Reading force field modification type file (frcmod)
> Reading title:
> remark goes here
> > loadamberprep hem.prep
> Loading Prep file: ./hem.prep
> (no charges read on atoms lines in HEM INT 0)
> WARNING - skipping extra charge in: HEM INT 0
> WARNING - skipping extra charge in: HEM INT 0
> 24 pairs of atoms within potential bonding distance
> 0 are not H-H pairs
> > loadamberprep hem.back.prep
> Loading Prep file: ./hem.back.prep
> (no charges read on atoms lines in HEM INT 0)
> WARNING - skipping extra charge in: HEM INT 0
> WARNING - skipping extra charge in: HEM INT 0
> 24 pairs of atoms within potential bonding distance
> 0 are not H-H pairs
> > m=loadpdb 1U13.pdb
> Loading PDB file: ./1U13.pdb
> Added missing heavy atom: .R<NSER 2>.A<OG 10>
> Added missing heavy atom: .R<ARG 85>.A<CG 8>
> Added missing heavy atom: .R<ARG 85>.A<CD 11>
> Added missing heavy atom: .R<ARG 85>.A<NE 14>
> Added missing heavy atom: .R<ARG 85>.A<CZ 16>
> Added missing heavy atom: .R<ARG 85>.A<NH1 17>
> Added missing heavy atom: .R<ARG 85>.A<NH2 20>
> Added missing heavy atom: .R<ARG 86>.A<CG 8>
> Added missing heavy atom: .R<ARG 86>.A<CD 11>
> Added missing heavy atom: .R<ARG 86>.A<NE 14>
> Added missing heavy atom: .R<ARG 86>.A<CZ 16>
> Added missing heavy atom: .R<ARG 86>.A<NH1 17>
> Added missing heavy atom: .R<ARG 86>.A<NH2 20>
> Added missing heavy atom: .R<ASP 207>.A<CG 8>
> Added missing heavy atom: .R<ASP 207>.A<OD1 9>
> Added missing heavy atom: .R<ASP 207>.A<OD2 10>
> Added missing heavy atom: .R<GLU 220>.A<CG 8>
> Added missing heavy atom: .R<GLU 220>.A<CD 11>
> Added missing heavy atom: .R<GLU 220>.A<OE1 12>
> Added missing heavy atom: .R<GLU 220>.A<OE2 13>
> Added missing heavy atom: .R<CTHR 434>.A<OXT 15>
> One sided connection. Residue: TP3 missing connect0 atom.
> total atoms in file: 3685
> Leap added 3853 missing atoms according to residue templates:
> 21 Heavy
> 3832 H / lone pairs
> > saveamberparm m 1u13.prmtop 1u13.inpcrd
> Checking Unit.
> WARNING: There is a bond of 16.983232 angstroms between:
> ------- .R<GLY 84>.A<C 6> and .R<ARG 85>.A<N 1>
> WARNING: There is a bond of 8.335559 angstroms between:
> ------- .R<PRO 206>.A<C 13> and .R<ASP 207>.A<N 1>
> WARNING: The unperturbed charge of the unit: -14.000000 is not zero.
>
> -- ignoring the warnings.
>
> Building topology.
> Building atom parameters.
> For atom: .R<HEM 435>.A<NA 2> Could not find type: NP
> For atom: .R<HEM 435>.A<NB 23> Could not find type: NO
> For atom: .R<HEM 435>.A<CBB 32> Could not find type: CX
> For atom: .R<HEM 435>.A<NC 39> Could not find type: NP
> For atom: .R<HEM 435>.A<CBC 48> Could not find type: CX
> For atom: .R<HEM 435>.A<ND 55> Could not find type: NO
You have to make sure that all atom names in your PDB file match the
corresponding atom names in the HEM library file.
If your HEM residue is topologically different than the HEM residue in
the library file you downloaded, it won't work.
HTH,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Thu Aug 21 2014 - 07:30:02 PDT
