Re: AMBER: problems in adding ACE and NME group

From: backy <backy.ibms.sinica.edu.tw>
Date: Wed, 27 Jun 2007 14:55:47 +0800

Hi, amber users:

Based on Melinda's suggestion, the pdb file was modified like this below. But the *.top file was still not available.

:(



backy





REMARK
ATOM 1 N ALA 1 70.146 65.827 40.009
ATOM 2 H1 ALA 1 69.336 66.290 40.398
ATOM 3 C ACE 1 70.907 65.903 40.670
ATOM 4 H3 ALA 1 69.929 64.849 39.886
ATOM 5 CA ALA 1 70.526 66.443 38.710
ATOM 6 HA ALA 1 71.550 66.812 38.798
ATOM 7 CB ALA 1 70.498 65.414 37.563


.
.
.
ATOM 2327 NE2 HID 149 72.425 63.869 32.001
ATOM 2328 CD2 HID 149 72.081 64.901 32.885
ATOM 2329 HD2 HID 149 72.158 64.871 33.964
ATOM 2330 C HID 149 73.678 68.044 32.727
ATOM 2331 O HID 149 74.527 67.959 31.808
ATOM 2332 N NME 149 73.966 67.822 33.927
TER
END





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.pdb
Warning: name change in pdb file residue 1 ;
 this residue is split into ALA and ACE.
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.
3 residues had naming warnings.
 There are split residues;
 residue sequence numbers will not correspond to those in the pdb.
  Added missing heavy atom: .R<NALA 1>.A<CA 5>
  Added missing heavy atom: .R<NALA 1>.A<CB 7>
  Added missing heavy atom: .R<NALA 1>.A<C 11>
  Added missing heavy atom: .R<NALA 1>.A<O 12>
Bond: Maximum coordination exceeded on .R<ACE 2>.A<HH31 1>
      -- setting atoms pert=true overrides default limits
  Added missing heavy atom: .R<ACE 2>.A<CH3 2>
  Added missing heavy atom: .R<ACE 2>.A<O 6>
Created a new atom named: H3 within residue: .R<ALA 3>
  Added missing heavy atom: .R<ALA 3>.A<N 1>
  Added missing heavy atom: .R<NME 152>.A<CH3 3>
  total atoms in file: 2332
  Leap added 22 missing atoms according to residue templates:
       8 Heavy
       14 H / lone pairs
  The file contained 1 atoms not in residue templates
Checking Unit.
WARNING: The unperturbed charge of the unit: 11.000000 is not zero.
FATAL: Atom .R<ALA 3>.A<H3 11> does not have a type.
Failed to generate parameters
Parameter file was not saved.
        Quit

 



  ----- Original Message -----
  From: Melinda Layten
  To: amber.scripps.edu
  Sent: Wednesday, June 27, 2007 4:02 AM
  Subject: Re: AMBER: problems in adding ACE and NME group


  You can also run leap with your normal 1-149 no capping groups, save the pdb file and in the new pdb rename H2 of res 1 to C of ACE and OXT of 149 to N of NME.
   
  Once leap runs correctly and you can visualize your molecule in VMD or similar, then start worrying about running sander.

  Melinda
   
  On 6/25/07, priya priya <priyaanand_27.yahoo.co.in> wrote:
    you can use xleap to add ACE and NME to cap the system

    backy < backy.ibms.sinica.edu.tw> wrote:
      Actually, how users cap the protein terminal?
      For example, by which kind of program to put the initial coordinates for ACE
      and NME groups?

      backy
      ----- Original Message -----
      From: "David A. Case"

      To:
      Sent: Thursday, June 21, 2007 1:10 PM
      Subject: Re: AMBER: problems in adding ACE and NME group


> On Thu, Jun 21, 2007, backy wrote:
>
>> If there is a need in placing the whole ACE and NME group, how should I
>> input their initial coordinations?
>
> This is a very rare thing to do, and Amber admitedly doesn't make it very
> easy. It isn't something I would recommend just "for practice".
>
> You might use a homology-modeling program to add alanine at both ends,
> then
> delete the atoms you don't need, and change the residue names to ACE and
> NME.
>
> ....dac
>
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Received on Sun Jul 01 2007 - 06:07:03 PDT
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