[gmx-users] add a group to an amino acid

hengame fallah hengame.fallah at gmail.com
Tue Nov 9 11:09:48 CET 2010


Dear Mark,

I edited my pdb like this:
...
ATOM     41  N   BOC     3      -1.862   5.210   5.333
ATOM     42  H   BOC     3      -2.325   4.344   5.618
ATOM     43  CA  BOC     3      -1.001   5.232   4.169
ATOM     44  HA1 BOC     3      -0.540   6.235   4.026
ATOM     45  HA2 BOC     3      -0.172   4.511   4.360
ATOM     46  CB  BOC     3      -1.797   4.794   2.924
ATOM     47  HB1 BOC     3      -2.244   3.809   3.204
ATOM     48  CG1 BOC     3      -2.976   5.730   2.589
ATOM     49  CD1 BOC     3      -1.231   3.466   0.845
ATOM     50  HD1 BOC     3      -2.070   2.790   1.081
ATOM     51  CD2 BOC     3       0.120   5.408   1.353
ATOM     52  HD2 BOC     3       0.357   6.277   1.986
ATOM     53  CE1 BOC     3      -0.471   3.236  -0.312
ATOM     54  HE1 BOC     3      -0.717   2.381  -0.964
ATOM     55  CE2 BOC     3       0.881   5.182   0.197
ATOM     56  HE2 BOC     3       1.706   5.870  -0.054
ATOM     57  CZ  BOC     3       0.591   4.093  -0.639
ATOM     58  CG2 BOC     3      -0.935   4.544   1.698
ATOM     59  HG1 BOC     3      -3.530   5.331   1.707
ATOM     60  HG2 BOC     3      -3.708   5.729   3.431
ATOM     61  C   BOC     3      -2.565   7.148   2.291
ATOM     62  O   BOC     3      -2.716   8.035   3.131
ATOM     63  Cl  BOC     3       1.525   3.816  -2.062
END

and my .rtp file for [ BOC ] is:

[ BOC ]
 [ atoms ]
     N    opls_238   -0.500     1
     H    opls_241    0.300     1
    CA    opls_224B  -0.005     1
   HA1    opls_140    0.060     1
   HA2    opls_140    0.060     1
    CB    opls_149    0.140     2
   HB1    opls_140    0.060     2
   CG1    opls_145   -0.115     2
   CD1    opls_145   -0.115     3
   HD1    opls_146    0.115     3
   CD2    opls_145   -0.115     4
   HD2    opls_146    0.115     4
   CE1    opls_145   -0.115     5
   HE1    opls_146    0.115     5
   CE2    opls_145   -0.115     6
   HE2    opls_146    0.115     6
    CZ    opls_145    0.885     7
    Cl    opls_264   -1.000     7
   CG2    opls_071   -0.005     8
   HG1    opls_140    0.060     8
   HG2    opls_140    0.060     8
     C    opls_235    0.700     9
     O    opls_236   -0.700     9
 [ bonds ]
     N     H
     N    CA
    CA   HA1
    CA   HA2
    CA    CB
    CB   HB1
    CB   CG1
    CB   CG2
   CG1   CD1
   CG1   CD2
   CD1   HD1
   CD1   CE1
   CD2   HD2
   CD2   CE2
   CE1   HE1
   CE1    CZ
   CE2   HE2
   CE2    CZ
    CZ    Cl
   CG2   HG1
   CG2   HG2
   CG2     C
     C     O
    -C     N

and still i got that error!

Fatal error:
Atom HB11 not found in rtp database in residue BOC, it looks a bit like HB1

On Tue, Nov 9, 2010 at 1:12 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  On 9/11/2010 8:19 PM, hengame fallah wrote:
>
> Thanks Justin,
> actually the protein that i want to simulate consists of two amino acids:
> PHE and BOC
> BOC is an unusual amino acid as you know.
> It has a Cl instead of HZ in PHE and has one extra CH2 in comparison to PHE
>
>
> So that probably means you'll have to pay care to the [bonds] section in
> the .rtp file. The only bonds GROMACS knows about are the ones in the .rtp.
> They have to be right. The errors below look like you haven't done it right.
>
>
>  I finally defined a residue BOC in opls .rtp file:
>
> [ BOC ]
>  [ atoms ]
>      N    opls_238   -0.500     1
>      H    opls_241    0.300     1
>     CA    opls_224B  -0.005     1
>    HA1    opls_140    0.060     1
>    HA2    opls_140    0.060     1
>     CB    opls_149    0.140     2
>    HB1    opls_140    0.060     2
>    CG1    opls_145   -0.115     2
>    CD1    opls_145   -0.115     3
>    HD1    opls_146    0.115     3
>    CD2    opls_145   -0.115     4
>    HD2    opls_146    0.115     4
>    CE1    opls_145   -0.115     5
>    HE1    opls_146    0.115     5
>    CE2    opls_145   -0.115     6
>    HE2    opls_146    0.115     6
>     CZ    opls_145    0.885     7
>     Cl    opls_264   -1.000     7
>    CG2    opls_071   -0.005     8
>    HG1    opls_140    0.060     8
>    HG2    opls_140    0.060     8
>      C    opls_235    0.700     9
>      O    opls_236   -0.700     9
>
> the ending part of my PDB is:
> ...
> ATOM     38  HE2 PHE     2      -6.946   8.455   4.409
> ATOM     39  CZ  PHE     2      -5.456  10.015   4.624
> ATOM     40  HZ  PHE     2      -5.887  10.646   3.828
> ATOM     41  N   BOC     3      -1.862   5.210   5.333
> ATOM     42  H   BOC     3      -2.325   4.344   5.618
> ATOM     43  CA  BOC     3      -1.001   5.232   4.169
> ATOM     44  HA1 BOC     3      -0.540   6.235   4.026
>
>
> HA2 is missing here, per your .rtp
>
>
> ATOM     45  CB  BOC     3      -1.797   4.794   2.924
> ATOM     46 HB1  BOC     3      -2.244   3.809   3.204
> ATOM     47  CG1 BOC     3      -2.976   5.730   2.589
> ATOM     48  CG2 BOC     3      -0.935   4.544   1.698
> ATOM     49  CD1 BOC     3      -1.231   3.466   0.845
> ATOM     50  HD1 BOC     3      -2.070   2.790   1.081
> ATOM     51  CD2 BOC     3       0.120   5.408   1.353
> ATOM     52  HD2 BOC     3       0.357   6.277   1.986
> ATOM     53  CE1 BOC     3      -0.471   3.236  -0.312
> ATOM     54  HE1 BOC     3      -0.717   2.381  -0.964
> ATOM     55  CE2 BOC     3       0.881   5.182   0.197
> ATOM     56  HE2 BOC     3       1.706   5.870  -0.054
> ATOM     57  CZ  BOC     3       0.591   4.093  -0.639
> ATOM     58  C   BOC     3      -2.565   7.148   2.291
> ATOM     59  O   BOC     3      -2.716   8.035   3.131
> ATOM     60  CL  BOC     3       1.525   3.816  -2.062
> ATOM     61  HA2 BOC     3      -0.172   4.511   4.360
> ATOM     62  HG1 BOC     3      -3.530   5.331   1.707
> ATOM     63  HG2 BOC     3      -3.708   5.729   3.431
>
> Now i got t this error:
> ...
> There are 1 chains and 0 blocks of water and 3 residues with 63 atoms
>
>   chain  #res #atoms
>   1 ' '     3     63
>
> All occupancy fields zero. This is probably not an X-Ray structure
> Opening library file /usr/share/gromacs/top/ffoplsaa.atp
> Atomtype 1
> Reading residue database... (ffoplsaa)
> Opening library file /usr/share/gromacs/top/ffoplsaa.rtp
> Residue 57
> Sorting it all out...
> Opening library file /usr/share/gromacs/top/ffoplsaa.hdb
> Opening library file /usr/share/gromacs/top/ffoplsaa-n.tdb
> Opening library file /usr/share/gromacs/top/ffoplsaa-c.tdb
>
> Back Off! I just backed up topol.top to ./#topol.top.69#
> Processing chain 1 (63 atoms, 3 residues)
> There are 3 donors and 3 acceptors
> There are 4 hydrogen bonds
> Checking for duplicate atoms....
> Opening library file /usr/share/gromacs/top/specbond.dat
> 7 out of 7 lines of specbond.dat converted succesfully
> N-terminus: NH3+
> C-terminus: COO-
> Now there are 3 residues with 68 atoms
> Making bonds...
> Warning: Long Bond (52-53 = 0.334847 nm)
> Warning: Long Bond (52-55 = 0.334912 nm)
> Warning: Long Bond (63-64 = 0.271173 nm)
> Warning: Long Bond (63-65 = 0.347808 nm)
> Warning: Long Bond (63-66 = 0.31288 nm)
>
>
> This is telling you the connectivity in your .rtp doesn't match the spatial
> arrangement very well. Go back and check the .rtp file.
>
>
> Opening library file /usr/share/gromacs/top/aminoacids.dat
>
> -------------------------------------------------------
> Program pdb2gmx, VERSION 4.0.7
> Source code file: ../../../../src/kernel/add_par.c, line: 233
>
> Fatal error:
> Atom HB11 not found in rtp database in residue BOC, it looks a bit like
> HB1
>
>
> pdb2gmx is probably hopelessly confused by now. Fix the other issues and
> try again.
>
> Mark
>
>
>  -------------------------------------------------------
> ...
>
> What should i do?
>
>
>
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