[gmx-users] File forcefield.itp, line 4 Last line read: '[ defaults ]' Invalid order for directive defaults

[Qing Lv]

The problem has been solved. I forgot to delete some entries when using .top file as .itp file.


Thanks,
Qing


At 2017-06-23 15:36:32, "Mark Abraham" <mark.j.abraham at gmail.com> wrote:
>Hi,
>
>You can't just paste together two topology files intended to stand alone
>e.g. because they have [defaults] sections. You can #include files, but
>they have to follow the structure of the example in chapter 5 of the manual
>(and every tutorial). Defaults, then atomtypes and parameters, then
>moleculetypes, then system.
>
>Mark
>
>On Fri, Jun 23, 2017 at 5:47 AM Qing Lv <lvqingjiejie at 163.com> wrote:
>
>> I changed the order of .itp file and put the "topol_ATP.itp" ahead of
>> protein.itp . However, I got the following errors this time:
>> Fatal error:
>> Syntax error - File forcefield.itp, line 6
>> Last line read:
>> '  1            1               no              1.0     1.0'
>> Found a second defaults directive.
>>
>>
>> P.S.
>> My topology file includes ATP, Protein, and Mg2+.  I tried to remove Mg2+
>> (probably inappropriate) but still got the same errors.
>>
>>
>> Thanks,
>> Qing
>>
>>
>>
>> At 2017-06-23 09:46:49, "Qing Lv" <lvqingjiejie at 163.com> wrote:
>> >Dear All,
>> >
>> >
>> >I am setting up a simulation of protein-ATP complex. I manually combined
>> the coordinates and topologies of the protein and ATP together, and ran
>> editconf and solvate successfully. However, when I ran grompp, errors
>> occurred:
>> >Syntax error - File forcefield.itp, line 4
>> >Last line read:
>> >'[ defaults ]'
>> >Invalid order for directive defaults
>> >
>> >
>> >I checked the .itp files I used and did not find "[ defaults ]" pattern.
>> How to fix it?
>> >Thanks,
>> >Qing
>> >--
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