[gmx-users] Error in energy groups

[masoud keramati]

it was wrong
i make new index that contain Non-Protein group.
my problem fix!

tnx

On Mon, Jul 25, 2016 at 12:08 AM, masoud keramati <keramati.ma3oud at gmail.com
> wrote:

> tnx Dr.Lemkul
>
> yes the problem was in the tc-grps.
> tc-grps        = Protein Non-Protein
> and there is no Non-Protein group in index file.
> it's true that i use System for tc-grps?
>
> On Sun, Jul 24, 2016 at 11:54 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>>
>> On 7/24/16 3:17 PM, masoud keramati wrote:
>>
>>> Hi all
>>>
>>> i have a protein with six chain.
>>> i create an index file that include each chain (chA chB ..)
>>> in mdp file i define energy groups such that:
>>> energygrps   = chA chD
>>>
>>> for grompp i used this command:
>>> gmx grompp -f md.mdp -c npt.gro -n chains.ndx -p topol.top -o A-D.tpr
>>>
>>> but i got this error:
>>> "Group Non-Protein referenced in the .mdp file was not found in the index
>>> file.
>>> Group names must match either [moleculetype] names or custom index group
>>> names, in which case you must supply an index file to the '-n' option
>>> of grompp "
>>>
>>> what's wrong with this?!
>>>
>>>
>> You have some setting that uses Non-Protein but you haven't got that in
>> your index file.  Check tc-grps as the most likely culprit.  If your index
>> file *only* contains the chains that you've specified, then you're going to
>> encounter problems.  In general, add groups that you need and leave the
>> default groups (System, Protein, Non-Protein, etc.) in place for ease of
>> use.
>>
>> -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.
>>
>
>