Re: [gmx-users] Error in energy groups

[masoud keramati]

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  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
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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> Gromacs Users mailing list
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Re: [gmx-users] Error in energy groups

[Justin Lemkul]

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

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

==
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[gmx-users] Error in energy groups

[masoud keramati]

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?!

thank for your help : )
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