Re: [AMBER] antechamber

From: 闫玉娜 <hiyanyuna.gmail.com>
Date: Thu, 21 Aug 2014 21:52:51 +0800

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
Parameter file was not saved.
>



2014-08-20 20:21 GMT+08:00 闫玉娜 <hiyanyuna.gmail.com>:

> Thank you much. I find it
>
>
> 2014-08-20 19:41 GMT+08:00 Jason Swails <jason.swails.gmail.com>:
>
> On Wed, 2014-08-20 at 10:31 +0800, 闫玉娜 wrote:
>> > Hi all,
>> > I have a small molecule named 'HEM'. I want to use antechamber to build
>> its
>> > parameters. I use the command 'antechamber -i HEM_ideal.pdb -fi pdb -o
>> > hem.mol2 -fo mol2 -c bcc -s 2 -nc 0'.But there are errors as follows:
>> >
>> >
>> > “Running: /home/yanyuna/Programs/amber11/bin/bondtype -j full -i
>> > ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac
>> >
>> >
>> >
>> > Running: /home/yanyuna/Programs/amber11/bin/atomtype -i
>> ANTECHAMBER_AC.AC0
>> > -o ANTECHAMBER_AC.AC -p gaff
>> >
>> > Total number of electrons: 305; net charge: 0
>> > INFO: Number of electrons is odd: 305
>> > Please check the total charge (-nc flag) and spin multiplicity (-m
>> > flag)
>> >
>> > Running: /home/yanyuna/Programs/amber11/bin/sqm -O -i sqm.in -o sqm.out
>> > Error: cannot run "/home/yanyuna/Programs/amber11/bin/sqm -O -i sqm.in
>> -o
>> > sqm.out" of bcc() in charge.c properly, exit”
>> >
>> > I have attached its structure file. How can I solve it? Thank you
>>
>> Amber error messages do not get much clearer than this. You requested a
>> QM calculation telling antechamber that the net charge was zero and the
>> multiplicity was 1. When the net charge is 0, then the number of
>> electrons is the same as the number of protons -- in this case 305. It
>> is impossible to have a singlet with an odd number of electrons, so you
>> get this error.
>>
>> What's more is that no charge method that uses a semi-empirical
>> Hamiltonian (like am1-bcc) can handle open-shell systems (like your
>> iron-containing Heme complex is). So you can't use antechamber unless
>> you first compute the electrostatic potential with Gaussian and ask for
>> "resp" charges.
>>
>> Alternatives are: look to see if your Heme complex has already been
>> parametrized (search for "amber heme" in Google and you will get lots of
>> hits). Use MCPB or R.E.D. to derive charges and force field parameters.
>>
>> HTH,
>> Jason
>>
>> --
>> Jason M. Swails
>> BioMaPS,
>> Rutgers University
>> Postdoctoral Researcher
>>
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>


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Received on Thu Aug 21 2014 - 07:00:04 PDT
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