Re: AMBER: problems in adding ACE and NME group

From: backy <backy.ibms.sinica.edu.tw>
Date: Wed, 20 Jun 2007 21:15:25 +0800

Hi:

but even I tried not to set idiel , the error messages are still there.

And I worried about if the setting of ACE and NME are correct?

Because the last 4 lines looks weird.



backy



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





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.scripps.edu
  Sent: Wednesday, June 20, 2007 7:28 PM
  Subject: Re: AMBER: problems in adding ACE and NME group


  one of your namelist variables is wrong, usually it is easiest
  to find this by removing them one by one until it runs, then you
  know which one was incorrect. in this case it might be that idiel is not
  a sander variable.



  On 6/20/07, backy <backy.ibms.sinica.edu.tw> wrote:
    Dear Amber users:

    I am using amber 9 and want to cap the N and C terminal for the given
    protein.
    So, in the given protein the first residue at position 1 and the last one at
    position 149 were modified by adding ACE and NME groups.


    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
    .

    .

    .

    ATOM 1182 CA HID A 149 72.111 68.499 32.373 1.00 0.00
    ATOM 1183 C HID A 149 73.534 68.060 32.700 1.00 0.00
    ATOM 1184 O HID A 149 74.355 67.976 31.762 1.00 0.00
    ATOM 1185 CB HID A 149 71.171 67.340 32.690 1.00 0.00
    ATOM 1186 CG HID A 149 71.681 66.008 32.234 1.00 0.00
    ATOM 1187 ND1 HID A 149 71.796 65.669 30.903 1.00 0.00
    ATOM 1188 CD2 HID A 149 72.104 64.928 32.935 1.00 0.00
    ATOM 1189 CE1 HID A 149 72.263 64.437 30.803 1.00 0.00
    ATOM 1190 N NME A 149 72.457 63.965 32.021 1.00 0.00


    Also, here below is the input file, sander.in_leo, for ironing out the poor
    placemats of these two gropes.



    min + md
    &cntrl imin = 1, irest=0, ibelly=1,
      ntx=1, idiel = 0, cut = 8.0, SCEE=1.2,
      ntpr=500, maxcyc=20000, ncyc=8000, drms=0.01
    &end
    Group input for restrained atoms
       50.0
    RES 1
    RES 151
    END
    END




    Finally, here comes the error messages like this:

    forrtl: severe (19): invalid reference to variable in NAMELIST input, unit
    5, file
    /mount/disk15/backy/system/RNA/Amber/RNA_bound/Backy/cap-1jbs-A-GB/sander.in_leo,
    line 3, position 14
    Image PC Routine Line Source
    sander 08560280 Unknown Unknown Unknown
    sander 0855FD78 Unknown Unknown Unknown
    sander 0852D0D9 Unknown Unknown Unknown
    sander 084F098C Unknown Unknown Unknown
    sander 084F0E2F Unknown Unknown Unknown
    sander 0850E440 Unknown Unknown Unknown
    sander 080E96B2 Unknown Unknown Unknown
    sander 080D040C Unknown Unknown Unknown
    sander 080D0155 Unknown Unknown Unknown
    sander 0804A5E8 Unknown Unknown Unknown
    Unknown 006BBDE3 Unknown Unknown Unknown
    sander 0804A4A1 Unknown Unknown Unknown




    Could anyone figure what's wrong?

    Thanks.





    backy



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Received on Sun Jun 24 2007 - 06:07:06 PDT
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