On 16/11/2010 9:04 PM, hengame fallah wrote:
Thank you very much, Mark!
Now i have errors from my .top file after grompp command.
The question is that why in pdb2gmx, editconf ,genbox and make_ndx
steps i don't see these errors:
...
processing topology...
Opening library file /usr/share/gromacs/top/ffoplsaa.itp
Opening library file /usr/share/gromacs/top/ffoplsaanb.itp
Opening library file /usr/share/gromacs/top/ffoplsaabon.itp
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
ERROR 1 [file topol.top, line 412]:
No default Angle types
ERROR 2 [file topol.top, line 567]:
No default Ryckaert-Bell. types
ERROR 3 [file topol.top, line 570]:
No default Ryckaert-Bell. types
ERROR 4 [file topol.top, line 573]:
No default Ryckaert-Bell. types
ERROR 5 [file topol.top, line 580]:
No default Ryckaert-Bell. types
ERROR 6 [file topol.top, line 581]:
No default Ryckaert-Bell. types
ERROR 7 [file topol.top, line 582]:
No default Ryckaert-Bell. types
Opening library file /usr/share/gromacs/top/spc.itp
Opening library file /usr/share/gromacs/top/ions.itp
Excluding 3 bonded neighbours molecule type 'Protein'
Excluding 2 bonded neighbours molecule type 'SOL'
NOTE 1 [file topol.top, line 664]:
System has non-zero total charge: 6.000000e-02
0.06 means your residue's charges do not add to zero, and they should.
processing coordinates...
double-checking input for internal consistency...
renumbering atomtypes...
converting bonded parameters...
There was 1 note
-------------------------------------------------------
Program grompp, VERSION 4.0.7
Source code file: ../../../../src/kernel/grompp.c, line: 986
Fatal error:
There were 7 errors in input file(s)
*topol.top:*
...
43 opls_238 3 BOC N 17 -0.5 14.0067 ; qtot 0.5
44 opls_241 3 BOC H 17 0.3
1.008 ; qtot 0.8
45 opls_283 3 BOC CA 17 0.04 12.011 ; qtot 0.84
46 opls_140 3 BOC HA1 17 0.06 1.008 ; qtot 0.9
47 opls_140 3 BOC HA2 17 0.06 1.008 ; qtot 0.96
48 opls_149 3 BOC CB 18 0.055 12.011 ; qtot 1.015
49 opls_140 3 BOC HB 18 0.06 1.008
; qtot 1.075
50 opls_145 3 BOC CG1 18 -0.115 12.011
; qtot 0.96
51 opls_145 3 BOC CD1 19 -0.115 12.011
; qtot 0.845
52 opls_146 3 BOC HD1 19 0.115 1.008
; qtot 0.96
53 opls_145 3 BOC CD2 20 -0.115 12.011
; qtot 0.845
54 opls_146 3 BOC HD2 20 0.115 1.008
; qtot 0.96
55 opls_145 3 BOC CE1 21 -0.115 12.011
; qtot 0.845
56 opls_146 3 BOC HE1 21 0.115 1.008
; qtot 0.96
57 opls_145 3 BOC CE2 22 -0.115 12.011
; qtot 0.845
58 opls_146 3 BOC HE2 22 0.115 1.008
; qtot 0.96
59 opls_145 3 BOC CZ 23 1 12.011
; qtot 1.96
60 opls_264 3 BOC Cl 23 -1
35.453 ; qtot 0.96
61 opls_224B 3 BOC CG2 24 -0.12 12.011 ; qtot 0.84
62 opls_140 3 BOC HG1 24 0.06 1.008 ; qtot 0.9
63 opls_140 3 BOC HG2 24 0.06 1.008 ; qtot 0.96
64 opls_271 3 BOC C 25 0.7 12.011 ; qtot 1.66
65 opls_272 3 BOC O1 25 -0.8 15.9994
; qtot 0.86
66 opls_272 3 BOC O2 25 -0.8 15.9994
; qtot 0.06
...
[ angles ]
...
line 412: 45 48 61 1
...
[ dihedrals ]
...
line 567: 43 45 48 61 3
...
line 570: 46 45 48 61 3
...
line 573: 47 45 48 61 3
...
line 580: 45 48 61 62 3
line 581: 45 48 61 63 3
line 582: 45 48 61 64 3
...
it seems that "45 48 61" is the problem. CA CB CG2
Where i should define angle type for it?
Those three atoms have types. The type of function to put on an angle
whose three atoms have given types is defined in the force field.
Evidently, there isn't one for the types of these atoms. This relates to
choosing your atom types properly, like I've said twice before now. Go
and look up their types in the .rtp, and then look up in the .atp what
environments the types for which they were parameterized, and see what
your non sequitur is.
Mark
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