AMBER Archive (2007)

Subject: Re: AMBER: problems in adding ACE and NME group

From: backy (backy_at_ibms.sinica.edu.tw)
Date: Thu Jun 21 2007 - 00:00:12 CDT

Here is all the details.

Thanks.

backy

print `$AMBERHOME/exe/tleap -f leanin\n`;

---------------leapin ---------------------------------------

source leaprc.ff03
set default PBradii bondi
trx = loadpdb 1jbs-A-wild.oo
saveamberparm trx 1jbs-A-wild.top 1jbs-A-wild.crd
quit

-----------------------------------------------------------

-I: Adding /home/.2/amber9/dat/leap/prep to search path.
-I: Adding /home/.2/amber9/dat/leap/lib to search path.
-I: Adding /home/.2/amber9/dat/leap/parm to search path.
-I: Adding /home/.2/amber9/dat/leap/cmd to search path.
-f: Source leapin.

Welcome to LEaP!
(no leaprc in search path)
Sourcing: ./leapin
----- Source: /home/.2/amber9/dat/leap/cmd/leaprc.ff03
----- Source of /home/.2/amber9/dat/leap/cmd/leaprc.ff03 done
Log file: ./leap.log
Loading parameters: /home/.2/amber9/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/.2/amber9/dat/leap/parm/frcmod.ff03
Reading force field modification type file (frcmod)
Reading title:
Duan et al ff03 phi psi torsions
Loading library: /home/.2/amber9/dat/leap/lib/ions94.lib
Loading library: /home/.2/amber9/dat/leap/lib/solvents.lib
Loading library: /home/.2/amber9/dat/leap/lib/all_nucleic94.lib
Loading library: /home/.2/amber9/dat/leap/lib/all_aminoct94.lib
Loading library: /home/.2/amber9/dat/leap/lib/all_aminont94.lib
Loading library: /home/.2/amber9/dat/leap/lib/all_amino03.lib
Using Bondi radii
Loading PDB file: ./1jbs-A-wild.oo
Warning: name change in pdb file residue 1 ;
 this residue is split into ACE and ALA.
Warning: name change in pdb file residue 149 ;
 this residue is split into HID and NME.
2 residues had naming warnings.
 There are split residues;
 residue sequence numbers will not correspond to those in the pdb.
Created a new atom named: N within residue: .R<ACE 1>
  Added missing heavy atom: .R<ACE 1>.A<O 6>
  Added missing heavy atom: .R<ACE 1>.A<C 5>
  Added missing heavy atom: .R<ACE 1>.A<CH3 2>
  Added missing heavy atom: .R<ALA 2>.A<N 1>
  Added missing heavy atom: .R<HID 150>.A<NE2 13>
Created a new atom named: NE2 within residue: .R<NME 151>
  Added missing heavy atom: .R<NME 151>.A<N 1>
  Added missing heavy atom: .R<NME 151>.A<CH3 3>
  total atoms in file: 1190
  Leap added 1153 missing atoms according to residue templates:
       7 Heavy
       1146 H / lone pairs
  The file contained 2 atoms not in residue templates
Checking Unit.
WARNING: There is a bond of 103.383324 angstroms between:
------- .R<ACE 1>.A<C 5> and .R<ALA 2>.A<N 1>
WARNING: The unperturbed charge of the unit: 10.000000 is not zero.
FATAL: Atom .R<ACE 1>.A<N 7> does not have a type.
FATAL: Atom .R<NME 151>.A<NE2 7> does not have a type.
Failed to generate parameters
Parameter file was not saved.
    Quit
 

  ----- Original Message -----
  From: Carlos Simmerling
  To: amber_at_scripps.edu
  Sent: Thursday, June 21, 2007 12:28 PM
  Subject: Re: AMBER: problems in adding ACE and NME group

  it would help if you provide leap input/output. is there any error or warning?

  On 6/21/07, backy <backy_at_ibms.sinica.edu.tw > wrote:
    by the way, this complete protein is a test case for me practicing the
    protein capping stuff.
    :)
    backy

    ----- Original Message -----
    From: "backy" <backy_at_ibms.sinica.edu.tw>
    To: < amber_at_scripps.edu>
    Sent: Thursday, June 21, 2007 11:54 AM
    Subject: Re: AMBER: problems in adding ACE and NME group

> If there is a need in placing the whole ACE and NME group, how should I
> input their initial coordinations?
> Thanks.
>
> backy
>
>
>
>
> ----- Original Message -----
> From: "David A. Case" <case_at_scripps.edu>
> To: < amber_at_scripps.edu>
> Sent: Wednesday, June 20, 2007 11:41 PM
> Subject: Re: AMBER: problems in adding ACE and NME group
>
>
>> On Wed, Jun 20, 2007, backy wrote:
>>
>>> Parameter file was not saved.
>> ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
>>
>> You had error in the leap step, never actually made a prmtop file.
>>
>>>
>>> ATOM 1 C ACE A 1 70.110 65.868 39.946 1.00 0.00
>>> ATOM 2 CA ALA A 1 70.537 66.473 38.657 1.00 0.00
>>> ATOM 3 C ALA A 1 69.639 67.664 38.316 1.00 0.00
>>> ATOM 4 O ALA A 1 68.434 67.654 38.604 1.00 0.00
>>> ATOM 5 CB ALA A 1 70.456 65.436 37.551 1.00 0.00
>>> ATOM 6 N THR A 2 70.232 68.687 37.711 1.00 0.00
>>> ATOM 7 CA THR A 2 69.495 69.875 37.320 1.00 0.00
>>> ATOM 8 C THR A 2 69.540 70.004 35.797 1.00 0.00
>>
>> You have to add an entire ACE residue (or at least the heavy atoms), not
>> just
>> one C atom. Also, you have two residues labelled "1" (ACE and ALA),
>> which
>> will confuse LEaP. Also, there is no N atom for the ALA.
>>
>> Don't try to run sander until you get LEaP running the way it should.
>>
>> ...good luck...dac
>>
>> p.s.: are you sure you want to add the capping groups to a complete
>> protein?
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>>
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>> Version: 7.5.472 / Virus Database: 269.9.1/854 - Release Date: 2007/6/19
>> ¤U¤È 01:12
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>>
>
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  Version: 7.5.472 / Virus Database: 269.9.1/857 - Release Date: 2007/6/20 $U$H 02:18

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