[gmx-users] more problems with building blocks and pdb2gmx

David van der Spoel spoel at xray.bmc.uu.se
Thu Nov 11 16:31:18 CET 2004


On Thu, 2004-11-11 at 15:50 +0100, gloria wrote:
> 
> 
> ______________________________________________________________________
> 
> Dear gromacs users,
> 
> i have a new building block inserted in ffG43a1.rtp, ffG43a1.hdb and
> aminoacids.dat. it should be working because it has been already
> tested, but when i try to run pdb2gmx i get an error, that is beyond
> my understanding.
You have some weirdness here: if you have an atom like C6a the hydrogen
should be called H6a, you cannot bind H6a to C4a. The O1 message is to
do with the termini database. Did you update the number of entries in
the aminoacids.dat file?
> 
> i know this has been repeated in the mailing list, but i cannot find
> what i am doing wrong, so please any suggestions will be welcomed. i
> have sticked here first the building block and then the error of
> pdb2gmx.
> 
> [ CYX ]
> [ atoms ]
>     N     N    -0.28000     0
>     H     H     0.28000     0
>    CA   CH1     0.00000     1
>    CB   CH2    -0.00000     2
>    SG     S    -0.20000     2
>    C1     C     0.40000     2
>    O1     O    -0.40000     2
>    C2     C    -0.40000     3
>    H2    HC     0.10000     3
>    C3     C     0.20000     4
>    H3    HC     0.10000     4
>   C1a     C    -0.30000     5
>   C2a     C    -0.14000     6
>   H2a    HC     0.14000     6
>   C6a     C    -0.14000     7
>   H6a    HC     0.14000     7
>   C3a     C    -0.34000     8
>   H3a    HC     0.14000     8
>   C5a     C    -0.34000     9
>   H5a    HC     0.14000     9
>   C4a     C     0.50000    10
>   O4a    OA    -0.60000    10
>     C     C       0.380    11
>     O     O      -0.380    11
> 
> [ bonds ]
>     N     H    gb_2
>     N    CA    gb_20
>    CA     C    gb_26
>     C     O    gb_4
>     C    +N    gb_9
>    CA    CB    gb_26
>    CB    SG  gb_30
>    SG    C1  gb_30
>    C1    O1  gb_4
>    C1    C2  gb_15
>    C2    H2  gb_3
>    C2    C3  gb_15
>    C3    H3  gb_3
>    C3   C1a  gb_15
>    C1a  C2a  gb_15
>    C1a  C6a  gb_15
>    C2a  H2a  gb_3
>    C6a  H6a  gb_3
>    C2a  C3a  gb_15
>    C6a  C5a  gb_15
>    C3a  H3a  gb_3
>    C5a  H5a  gb_3
>    C3a  C4a  gb_15
>    C5a  C4a  gb_15
>    C4a  O4a  gb_12
> 
> [ exclusions ]
>    C1   C1a
>    C1   H3
>    O1   C3
>    O1   H2
>    SG   C3
>    SG   H2
>    CB   O1
>    CB   C2
>    C2   C2a
>    C2   C6a
>    H2    H3
>    H2   C1a
>    H3   C2a
>    H3   C6a
>    C3   H2a
>    C3   H6a
>    C3   C3a
>    C3   C5a
>   C1a   H3a
>   C1a   H5a
>   C1a   C4a
>   C2a   H6a
>   C2a   C5a
>   C2a   O4a
>   H2a   C6a
>   H2a   H3a
>   H2a   C4a
>   C6a   C3a
>   C6a   O4a
>   H6a   H5a
>   H6a   C4a
>   C3a   H5a
>   H3a   C5a
>   H3a   O4a
>   H5a   O4a
> 
> [ angles ]
> ;  ai    aj    ak   gromos type
>    -C     N     H     ga_31
>     H     N    CA     ga_17
>    -C     N    CA     ga_30
>     N    CA     C     ga_12
>    CA     C    +N     ga_18
>    CA     C     O     ga_29
>     O     C    +N     ga_32
>     N    CA    CB     ga_12
>     C    CA    CB     ga_12
>    CA    CB    SG     ga_15
>     CB   SG    C1  ga_3
>     SG   C1    O1  ga_29
>     SG   C1    C2  ga_15
>     O1   C1    C2  ga_29
>     C1   C2    H2  ga_24
>     C1   C2    C3  ga_26
>     H2   C2    C3  ga_24
>     C2   C3    H3  ga_24
>     C2   C3   C1a  ga_26
>     H3   C3   C1a  ga_24
>     C3  C1a   C2a  ga_26
>     C3  C1a   C6a  ga_26
>    C2a  C1a   C6a  ga_26
>    C1a  C2a   H2a  ga_24
>    C1a  C2a   C3a  ga_26
>    H2a  C2a   C3a  ga_24
>    C1a  C6a   H6a  ga_24
>    C1a  C6a   C5a  ga_26
>    H6a  C6a   C5a  ga_24
>    C2a  C3a   H3a  ga_24
>    C2a  C3a   C4a  ga_26
>    H3a  C3a   C4a  ga_24
>    C6a  C5a   H5a  ga_24
>    C6a  C5a   C4a  ga_26
>    H5a  C5a   C4a  ga_24
>    C3a  C4a   C5a  ga_26
>    C3a  C4a   O4a  ga_26
>    C5a  C4a   O4a  ga_26
> 
> [ impropers ]
> ;  ai aj    ak    al   gromos type
>     N    -C    CA     H     gi_1
>     C    CA    +N     O     gi_1
>    CA     N     C    CB     gi_2
>   C1a   C2a   C6a    C3     gi_1
>   C6a   C1a   C2a   C3a     gi_1
>   C2a   C1a   C6a   C5a     gi_1
>   C1a   C2a   C3a   C4a     gi_1
>   C1a   C6a   C5a   C4a     gi_1
>   C2a   C3a   C4a   C5a     gi_1
>   C6a   C5a   C4a   C3a     gi_1
>   C2a   C1a   C3a   H2a     gi_1
>   C6a   C1a   C5a   H6a     gi_1
>   C3a   C4a   C2a   H3a     gi_1
>   C5a   C4a   C6a   H5a     gi_1
>   C4a   C3a   C5a   O4a     gi_1
> 
> [ dihedrals ]
> ;  ai    aj    ak    al   gromos type
>   -CA    -C     N    CA     gd_4
>    -C     N    CA     C     gd_19
>     N    CA     C    +N     gd_20
>     N    CA    CB    SG     gd_17
>    CB    SG    C1    C2     ga_15
>    SG    C1    C2    C3     ga_15
>    C1    C2    C3   C1a     ga_15
>    C2    C3   C1a   C2a     ga_15
> 
> <<put in ffG43a1.hdb>>
> 
> CYX     7
>         1       1       N       -C      CA
>         1       1       C2a     C1a     C3a
>         1       1       C6a     C1a     C5a
>         1       1       C3a     C2a     C4a
>         1       1       C5a     C6a     C4a
>         1       1       C2      C1      C3
>         1       1       C3      C2      C1a
> 
> <<add in aminoacids.dat the CYX residue and increase the number at the
> top of the file>>
> 
> 
> [ CYX ]
> ; order husslet to match Sam de Visser's CA space....
> [ atoms ]
>     N     N    -0.28000     0
>     H     H     0.28000     0
>    CA   CH1     0.00000     1
>    CB   CH2    -0.00000     2
>    SG     S    -0.20000     2
>    C1     C     0.40000     2
>    O1     O    -0.40000     2
>    C2     C    -0.40000     3
>    H2    HC     0.10000     3
>    C3     C     0.20000     4
>    H3    HC     0.10000     4
>   C1a     C    -0.30000     5
>   C2a     C    -0.14000     6
>   H2a    HC     0.14000     6
>   C6a     C    -0.14000     7
>   H6a    HC     0.14000     7
>   C3a     C    -0.34000     8
>   H3a    HC     0.14000     8
>   C5a     C    -0.34000     9
>   H5a    HC     0.14000     9
>   C4a     C     0.50000    10
>   O4a    OA    -0.60000    10
>     C     C       0.380    11
>     O     O      -0.380    11
> 
> [ bonds ]
>     N     H    gb_2
>     N    CA    gb_20
>    CA     C    gb_26
>     C     O    gb_4
>     C    +N    gb_9
>    CA    CB    gb_26
>    CB    SG  gb_30
>    SG    C1  gb_30
>    C1    O1  gb_4
>    C1    C2  gb_15
>    C2    H2  gb_3
>    C2    C3  gb_15
>    C3    H3  gb_3
>    C3   C1a  gb_15
>    C1a  C2a  gb_15
>    C1a  C6a  gb_15
>    C2a  H2a  gb_3
>    C6a  H6a  gb_3
>    C2a  C3a  gb_15
>    C6a  C5a  gb_15
>    C3a  H3a  gb_3
>    C5a  H5a  gb_3
>    C3a  C4a  gb_15
>    C5a  C4a  gb_15
>    C4a  O4a  gb_12
> 
> [ exclusions ]
>    C1   C1a
>    C1   H3
>    O1   C3
>    O1   H2
>    SG   C3
>    SG   H2
>    CB   O1
>    CB   C2
>    C2   C2a
>    C2   C6a
>    H2    H3
>    H2   C1a
>    H3   C2a
>    H3   C6a
>    C3   H2a
>    C3   H6a
>    C3   C3a
>    C3   C5a
>   C1a   H3a
>   C1a   H5a
>   C1a   C4a
>   C2a   H6a
>   C2a   C5a
>   C2a   O4a
>   H2a   C6a
>   H2a   H3a
>   H2a   C4a
>   C6a   C3a
>   C6a   O4a
>   H6a   H5a
>   H6a   C4a
>   C3a   H5a
>   H3a   C5a
>   H3a   O4a
>   H5a   O4a
> 
> [ angles ]
> ;  ai    aj    ak   gromos type
>    -C     N     H     ga_31
>     H     N    CA     ga_17
>    -C     N    CA     ga_30
>     N    CA     C     ga_12
>    CA     C    +N     ga_18
>    CA     C     O     ga_29
>     O   C    +N     ga_32
>     N    CA    CB     ga_12
>     C    CA    CB     ga_12
>    CA    CB    SG     ga_15
>     CB   SG    C1  ga_3
>     SG   C1    O1  ga_29
>     SG   C1    C2  ga_15
>     O1   C1    C2  ga_29
>     C1   C2    H2  ga_24
>     C1   C2    C3  ga_26
>     H2   C2    C3  ga_24
>     C2   C3    H3  ga_24
>     C2   C3   C1a  ga_26
>     H3   C3   C1a  ga_24
>     C3  C1a   C2a  ga_26
>     C3  C1a   C6a  ga_26
>    C2a  C1a   C6a  ga_26
>    C1a  C2a   H2a  ga_24
>    C1a  C2a   C3a  ga_26
>    H2a  C2a   C3a  ga_24
>    C1a  C6a   H6a  ga_24
>    C1a  C6a   C5a  ga_26
>    H6a  C6a   C5a  ga_24
>    C2a  C3a   H3a  ga_24
>    C2a  C3a   C4a  ga_26
>    H3a  C3a   C4a  ga_24
>    C6a  C5a   H5a  ga_24
>    C6a  C5a   C4a  ga_26
>    H5a  C5a   C4a  ga_24
>    C3a  C4a   C5a  ga_26
>    C3a  C4a   O4a  ga_26
>    C5a  C4a   O4a  ga_26
> 
> [ impropers ]
> ;  ai    aj    ak    al   gromos type
>     N    -C    CA     H     gi_1
>     C    CA    +N     O     gi_1
>    CA     N     C    CB     gi_2
>   C1a   C2a   C6a    C3     gi_1
>   C6a   C1a   C2a   C3a     gi_1
>   C2a   C1a   C6a   C5a     gi_1
>   C1a   C2a   C3a   C4a     gi_1
>   C1a   C6a   C5a   C4a     gi_1
>   C2a   C3a   C4a   C5a     gi_1
>   C6a   C5a   C4a   C3a     gi_1
>   C2a   C1a   C3a   H2a     gi_1
>   C6a   C1a   C5a   H6a     gi_1
>   C3a   C4a   C2a   H3a     gi_1
>   C5a   C4a   C6a   H5a     gi_1
>   C4a   C3a   C5a   O4a     gi_1
> 
> [ dihedrals ]
> ;  ai    aj    ak    al   gromos type
>   -CA    -C     N    CA     gd_4
>    -C     N    CA     C     gd_19
>     N    CA     C    +N     gd_20
>     N    CA    CB    SG     gd_17
>    CB    SG    C1    C2     ga_15
>    SG    C1    C2    C3     ga_15
>    C1    C2    C3   C1a     ga_15
>    C2    C3   C1a   C2a     ga_15
> 
> <<put in ffG43a1.hdb>>
> 
> CYX     7
>         1       1       N       -C      CA
>         1       1       C2a     C1a     C3a
>         1       1       C6a     C1a     C5a
>         1       1       C3a     C2a     C4a
>         1       1       C5a     C6a     C4a
>         1       1       C2      C1      C3
>         1       1       C3      C2      C1a
> 
> <<add in aminoacids.dat the CYX residue and increase the number at the
> top of the file>>
> 
> -------------------------------------- pdb2gmx error
> -----------------------------
> WARNING: atom O1 is missing in residue CYX 44 in the pdb file
> 
> 
> WARNING: atom H2a is missing in residue CYX 44 in the pdb file
>          You might need to add atom H2a to the hydrogen database of
> residue CYX
>          in the file ff???.hdb (see the manual)
> 
> 
> WARNING: atom H6a is missing in residue CYX 44 in the pdb file
>          You might need to add atom H6a to the hydrogen database of
> residue CYX
>          in the file ff???.hdb (see the manual)
> 
> 
> WARNING: atom H3a is missing in residue CYX 44 in the pdb file
>          You might need to add atom H3a to the hydrogen database of
> residue CYX
>          in the file ff???.hdb (see the manual)
> 
> 
> WARNING: atom H5a is missing in residue CYX 44 in the pdb file
>          You might need to add atom H5a to the hydrogen database of
> residue CYX
>          in the file ff???.hdb (see the manual)
> 
> There were 5 missing atoms in molecule Protein
> Number of bonds was 1063, now 1058
> Generating angles, dihedrals and pairs...
> Fatal error: atom name O1 not found in residue CYX 44 while generating
> exclusions
> ----------------------------
> and of course i have these atoms in the pdb file.  as force field i am
> using GROMOS96 43a1 Forcefield 
> 
> can it be because i am using the new version of gromacs, 3.2.1? or
> this has nothing to do?
> 
> 
> thank you 
> 
> gloria
> 
> 
> 
> 
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-- 
David van der Spoel <spoel at xray.bmc.uu.se>




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