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

hengame fallah hengame.fallah at gmail.com
Tue Nov 9 12:10:31 CET 2010


This is .rtp for [PHE] in opls:

[ PHE ]
 [ atoms ]
     N    opls_238   -0.500     1
     H    opls_241    0.300     1
    CA    opls_224B   0.140     1
    HA    opls_140    0.060     1
    CB    opls_149   -0.005     2
   HB1    opls_140    0.060     2
   HB2    opls_140    0.060     2
    CG    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   -0.115     7
    HZ    opls_146    0.115     7
     C    opls_235    0.500     8
     O    opls_236   -0.500     8
 [ bonds ]
     N     H
     N    CA
    CA    HA
    CA    CB
    CA     C
    CB   HB1
    CB   HB2
    CB    CG
    CG   CD1
    CG   CD2
   CD1   HD1
   CD1   CE1
   CD2   HD2
   CD2   CE2
   CE1   HE1
   CE1    CZ
   CE2   HE2
   CE2    CZ
    CZ    HZ
     C     O
    -C     N

and i got the charges by Gaussian.
I'm very confused now [?]
On Tue, Nov 9, 2010 at 2:13 PM, Mark Abraham <Mark.Abraham at anu.edu.au>wrote:

>  On 9/11/2010 9:09 PM, hengame fallah wrote:
>
> 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
>
>
> a) This structure is phenylalanine with *two* backbone methylene spacers,
> not the one you said in a previous email
> b) Your charge groups are wrong (e.g. number 2)
> c) Your charges are doubtful (CG1 is negative???)
> d) Your atom types are worth checking (should the two backbone methylene
> carbons have those types?)
> e) The atom ordering of the coordinate file and .rtp file need to match
> f) The atom coordinates do not correspond to the atom labels they are given
> - presumably you got another bunch of "long bond" warnings that you didn't
> include in your last email.
>
> Mark
>
>
>
> 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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