[gmx-users] Error with CHARMM36 force field

[laurenmr]

Hi Justin,

Thanks for the reply. Will download now.

Thanks,

Lauren


On 13/03/2018 17:50, Justin Lemkul wrote:
>
>
> On 3/13/18 5:47 AM, laurenmr wrote:
>> Hi Mark,
>>
>> Thanks for the reply. I will contact the relevant person!
>>
>
> This was a bug very briefly when the latest tarball went online. I 
> fixed it months ago.
>
> Please just download the latest tarball from 
> http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs.
>
> -Justin
>
>> Thanks,
>>
>> Lauren
>>
>>
>> On 13/03/2018 17:40, Mark Abraham wrote:
>>> Hi,
>>>
>>> Yes, I guess it must be somehow incompatible. Maybe it worked with 
>>> an older
>>> version of GROMACS that worked differently - the mdp handling has 
>>> had some
>>> cleaning up over time, and some buggy behaviours may have been
>>> inadvertently depended on. Perhaps this should be brought to the 
>>> attention
>>> of whoever maintains that file.
>>>
>>> Mark
>>>
>>> On Tue, Mar 13, 2018 at 10:17 AM laurenmr <laurenmr at bii.a-star.edu.sg>
>>> wrote:
>>>
>>>> Hi Mark,
>>>>
>>>> Thanks for the reply.
>>>>
>>>> I use GROMACS-5.1.4 and I just use standard Linux editors. Please find
>>>> my mdp file attached.
>>>>
>>>> When I check in the file "old_c36_cmap.itp" I do find very long 
>>>> lines (>
>>>> 4095 characters). Could this mean that this force field file is not
>>>> compatible with this version of GROMACS?
>>>>
>>>> Thanks,
>>>>
>>>> Lauren
>>>>
>>>>
>>>> On 13/03/2018 17:07, Mark Abraham wrote:
>>>>> Hi,
>>>>>
>>>>> What version of GROMACS is this? Did you edit your file using an
>>>> unsuitable
>>>>> editor, such as anything on Windows?
>>>>>
>>>>> Mark
>>>>>
>>>>> On Tue, Mar 13, 2018 at 9:20 AM laurenmr <laurenmr at bii.a-star.edu.sg>
>>>> wrote:
>>>>>> Hi Gromacs Users,
>>>>>>
>>>>>> I have downloaded the latest version of the CHARMM36M force 
>>>>>> field. My
>>>>>> aim is to compare a simulation using CHARMM36M and CHARMM36. In the
>>>>>> forcefield.itp there is an 'if' statement allowing the user to 
>>>>>> switch to
>>>>>> the old CHARMM36 force field by directing to the old cmap itp:
>>>>>>
>>>>>> ; Allow the user to specify CHARMM36 parameters, instead
>>>>>> ; Default behavior is to use CHARMM36m
>>>>>> #ifdef USE_OLD_C36
>>>>>> #include "old_c36_cmap.itp"
>>>>>> #else
>>>>>> #include "cmap.itp"
>>>>>> #endif
>>>>>>
>>>>>> However, when I include "define = -DUSE_OLD_C36" in my .mdp file I
>>>>>> receive this error at the grompp command:
>>>>>>
>>>>>> Fatal error:
>>>>>> An input file contains a line longer than 4095 characters, while the
>>>>>> buffer passed to fgets2 has size 4095. The line starts with: 'C 
>>>>>> NH1 CT1
>>>>>> C NH1 1 24'
>>>>>>
>>>>>> Could anyone suggest a way around this or should I download an older
>>>>>> version of CHARMM36 (before CHARMM36M)?
>>>>>>
>>>>>> Thanks in advance for the help!
>>>>>>
>>>>>> Lauren
>>>>>>
>>>>>>
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>