[gmx-users] cgenff CTAB

[xy21hb]

Dear Justin,


I fixed the naming problem as you said. Many thanks for your help.
However, the Br- ion in the original pdb does not appear in the converted structure.
I wonder how I can introduce it to the CHARMM ff in gromacs by changing the ions.itp file.


Thanks,


Yao








At 2016-03-30 06:52:21, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>
>
>On 3/29/16 6:32 PM, xy21hb wrote:
>>
>> https://www.dropbox.com/s/bptog3lgtyp9qt2/CTAB.zip?dl=0
>>
>> Dear Justin,
>>
>>
>> Above is the link to the mol2 and str files.
>> I checked the naming of the input files and the same error remained.
>>
>
>It's exactly as I expected; in the stream file you have:
>
>RESI /scrat
>
>and the .mol2 file has a residue named "MOL1" so it doesn't match.
>
>-Justin
>
>>
>> Thanks,
>>
>>
>> Yao
>>
>>
>>
>>
>>
>> At 2016-03-30 05:42:25, "Justin Lemkul" <jalemkul at vt.edu> wrote:
>>>
>>>
>>> On 3/29/16 5:40 PM, xy21hb wrote:
>>>> Dear all,
>>>> I am patching cetyltrimethylammonium bromide (ctab) by cgenff for CHARMM36 force field in GROMACS.
>>>> However, it always gives the wrong error message, saying that the number of atoms does not match the .top.
>>>> I wonder what could be the reason for this problem.
>>>
>>> Usually this means your residue name is specified incorrectly.  Check that your
>>> command line, .mol2, and RESI specification match.
>>>
>>>> Attached are .mol2 and .str files.
>>>
>>> The list does not accept attachments.  If you need to share files, upload them
>>> somewhere and provide a URL.
>>>
>>> -Justin
>>>
>>> --
>>> ==================================================
>>>
>>> Justin A. Lemkul, Ph.D.
>>> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>>>
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>
>-- 
>==================================================
>
>Justin A. Lemkul, Ph.D.
>Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
>Department of Pharmaceutical Sciences
>School of Pharmacy
>Health Sciences Facility II, Room 629
>University of Maryland, Baltimore
>20 Penn St.
>Baltimore, MD 21201
>
>jalemkul at outerbanks.umaryland.edu | (410) 706-7441
>http://mackerell.umaryland.edu/~jalemkul
>
>==================================================
>-- 
>Gromacs Users mailing list
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