[gmx-users] Error with CHARMM36 force field

[Justin Lemkul]

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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>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

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