[gmx-users] cgenff CTAB

[Justin Lemkul]

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
>>
>> 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
>>
>> * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-request at gromacs.org.

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

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

==================================================