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

gloria gloria at nmr.chem.uu.nl
Thu Nov 11 15:50:14 CET 2004


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.

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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