[gmx-users] grompp: "invalid bond type" error

Olivia Waring owaring at princeton.edu
Tue Nov 1 23:00:35 CET 2011


Thank you so much for your quick reply!

Below please find my topology file:


; Include forcefield parameters
#include "hautklein.ff/forcefield.itp"

[ moleculetype ]
; Name            nrexcl
Protein_chain_1     3

[ atoms ]
;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB
   chargeB      massB
; residue   0 ALK rtp ALK  q  0.0
     1        CH3      0    ALK    CH3      1          0     15.035   ;
qtot 0
     2        CH2      0    ALK   CH2A      2          0     14.027   ;
qtot 0
     3        CH2      0    ALK   CH2B      3          0     14.027   ;
qtot 0
     4        CH2      0    ALK   CH2C      4          0     14.027   ;
qtot 0
     5        CH2      0    ALK   CH2D      5          0     14.027   ;
qtot 0
     6        CH2      0    ALK   CH2E      6          0     14.027   ;
qtot 0
     7        CH2      0    ALK   CH2F      7          0     14.027   ;
qtot 0
     8        CH2      0    ALK   CH2G      8          0     14.027   ;
qtot 0
     9        CH2      0    ALK   CH2H      9          0     14.027   ;
qtot 0
    10        CH2      0    ALK   CH2I     10          0     14.027   ;
qtot 0
    11        CH2      0    ALK   CH2J     11          0     14.027   ;
qtot 0
    12        CH2      0    ALK   CH2K     12          0     14.027   ;
qtot 0
    13          S      0    ALK      S     13          0      32.06   ;
qtot 0

[ bonds ]
;  ai    aj funct            c0            c1            c2            c3
    1     2     1
    2     3     1
    3     4     1
    4     5     1
    5     6     1
    6     7     1
    7     8     1
    8     9     1
    9    10     1
   10    11     1
   11    12     1
   12    13     1

[ pairs ]
;  ai    aj funct            c0            c1            c2            c3
    1     4     1
    2     5     1
    3     6     1
    4     7     1
    5     8     1
    6     9     1
    7    10     1
    8    11     1
    9    12     1
   10    13     1

[ angles ]
;  ai    aj    ak funct            c0            c1            c2
 c3
    1     2     3     1
    2     3     4     1
    3     4     5     1
    4     5     6     1
    5     6     7     1
    6     7     8     1
    7     8     9     1
    8     9    10     1
    9    10    11     1
   10    11    12     1
   11    12    13     1

[ dihedrals ]
;  ai    aj    ak    al funct            c0            c1            c2
       c3            c4            c5
    1     2     3     4     3
    2     3     4     5     3
    3     4     5     6     3
    4     5     6     7     3
    5     6     7     8     3
    6     7     8     9     3
    7     8     9    10     3
    8     9    10    11     3
    9    10    11    12     3
   10    11    12    13     3

[ constraints ]
;   i     j     funct   b0
    1     2     1       0.0153
    2     3     1       0.0153
    3     4     1       0.0153
    4     5     1       0.0153
    5     6     1       0.0153
    6     7     1       0.0153
    7     8     1       0.0153
    8     9     1       0.0153
    9     10    1       0.0153
    10    11    1       0.0153
    11    12    1       0.0153
    12    13    1       0.0182

; Include Position restraint file
#ifdef POSRES
#include "posre.itp"
#endif

[ system ]
; Name
Protein

[ molecules ]
; Compound        #mols
Protein_chain_1     1

Does this help?

Thanks so much again,
Olivia

On Tue, Nov 1, 2011 at 5:49 PM, Justin A. Lemkul <jalemkul at vt.edu> wrote:

>
>
> Olivia Waring wrote:
>
>> Dear Gromacs users,
>>
>> First of all, many thanks to Justin for his assistance with my previous
>> question.
>>
>> I have defined a new residue type in the oplsaa force field, changing the
>> aminoacids.rtp file accordingly. pdb2gmx worked just fine; but when I try
>> to preprocess, I get the following output:
>> WARNING 1 [file ffbonded.itp, line 58]:
>>  Overriding Bond parameters.
>>
>>  old: 0.1229 476976 0.1229 476976
>>  new: C     O      1    0.13270   179075.2
>>
>>
>> WARNING 2 [file ffbonded.itp, line 64]:
>>  Overriding Bond parameters.
>>
>>  old: 0.1522 265266 0.1522 265266
>>  new: C    CT      1    0.14950   265265.6
>>
>>
>> WARNING 3 [file ffbonded.itp, line 67]:
>>  Overriding Bond parameters.
>>
>>  old: 0.149 334720 0.149 334720
>>  new: CA    C      1    0.14240   392459.2
>>
>>
>> WARNING 4 [file ffbonded.itp, line 73]:
>>  Overriding Bond parameters.
>>
>>  old: 0.1419 374050 0.1419 374050
>>  new: C    CB      1    0.14240   392459.2
>>
>>
> These four warnings suggest you're using values for bonded parameters that
> conflict with those present in the force field.  If you have reason to do
> this, then there's no problem, per se.  But be aware that you're using
> parameters the force field does not expect.
>
>
>
>> ------------------------------**-------------------------
>> Program grompp, VERSION 4.5.4
>> Source code file: topdirs.c, line: 76
>>
>> Fatal error:
>> Invalid bond type 0
>> For more information and tips for troubleshooting, please check the
>> GROMACS
>> website at http://www.gromacs.org/**Documentation/Errors<http://www.gromacs.org/Documentation/Errors>
>>
>>
>> The error is rather cryptic, and I'm having trouble tracking it down... I
>> even went to the source code (topdirs.c), but I'm still not sure where
>> exactly this "invalid bond type" is being defined.
>>
>
> This error suggests a more fundamental problem in your topology, but
> without seeing the topology, there's little more that can be said.
>
> -Justin
>
> --
> ==============================**==========
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.**vt.edu/Pages/Personal/justin<http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin>
>
> ==============================**==========
> --
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-- 
Olivia Waring (王维娅)
Princeton University '12
AB Chemistry
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