[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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