[gmx-users] RE: No default G96 Bond types error

[Mark Abraham]

Kukol, Andreas wrote:
> Hi,
> 
> Finally I found the reason for the error:
> 
> A space is required between the forcefield parameter code and the semicolon indicating a comment, i.e.:
> 
> No default G96Bond types error:
>>    31    32     2    gb_18; C-O ether bond  <- line 88
> 
> Works fine:
>>    31    32     2    gb_18 ; C-O ether bond  <- line 88
>                            ^^^
> This is a new problem with Gromacs4.

That's a bug, either with the cpp replacement or the line parsing for 
bond types. Please file a Bugzilla here http://bugzilla.gromacs.org

Mark

>> I get the following grompp error message with Gromacs 4.05 (but not with
>> Gromacs 3.2.1):
>> ************************
>> ...
>> Opening library file /usr/local/gromacs4/share/gromacs/top/ffG53a6bon.itp
>> Opening library file /usr/local/gromacs4/share/gromacs/top/ff_dum.itp
>> Generated 165 of the 1596 non-bonded parameter combinations
>>
>> ERROR 1 [file dhpc_53a6_3.itp, line 88]:
>>   No default G96Bond types
>>
>> ERROR 2 [file dhpc_53a6_3.itp, line 89]:
>>   No default G96Bond types
>>
>> Opening library file /usr/local/gromacs4/share/gromacs/top/spc.itp
>> Excluding 3 bonded neighbours molecule type 'DHPC'
>> ...
>> ...
>> ------------------------------------------------------
>> Program grompp4, VERSION 4.0.5
>> Source code file: grompp.c, line: 986
>>
>> Fatal error:
>> There were 2 errors in input file(s)
>> *******************
>>
>> I can't find any problem in the grompp log file (extract shown below):
>> *****************
>> dhpc_53a6_3.itp :   88 :    31    32     2    gb_18; C-O ether bond
>> push_bondnow: nr = 30
>> dhpc_53a6_3.itp :   89 :    32    33     2    gb_18; C-O ether bond
>> push_bondnow: nr = 31
>> dhpc_53a6_3.itp :   90 :    33    34     2    gb_27
>> push_bondnow: nr = 32
>> *****************
>>
>> Furthermore, the gb_18 bond type is used previously in line 70 and 72,
>> without error message, but lines 88 and 89 give this error. Here my itp-
>> file:
>> *****************
>>    13    14     2    gb_18 ; C-O ether      <- line 70
>>    13    31     2    gb_27
>>    14    15     2    gb_18 ; C-O ether bond <- line 72
>> ...
>> ...
>>    31    32     2    gb_18; C-O ether bond  <- line 88
>>    32    33     2    gb_18; C-O ether bond  <- line 89
>> *************
>>
>> Is this a grompp 4.05 problem or am I doing something wrong here ?
>>
>> Many thanks
>> Andreas
> 
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