[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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