[gmx-users] error in index file

[Justin Lemkul]

On 4/3/18 5:50 AM, Joe Jordan wrote:
> Gromacs 4.6 is no longer supported, so I would recommend upgrading to 2018
> and using gmx select. Short of that, if you just run make_ndx and don't use
> a selection sting you will get a group corresponding to NAP with the right
> number of atoms.

Neither gmx select nor gmx make_ndx should be necessary here. All 
defined [moleculetypes] are default index groups. The ligand should show 
up as a choice from any GROMACS program without needing an index file at 
all.

-Justin

> On Tue, Apr 3, 2018 at 11:41 AM, abhisek Mondal <abhisek.mndl at gmail.com>
> wrote:
>
>> I'm using v4.6.2
>>
>> $make_ndx -f npt.gro
>>
>>> r 306 (residue num of ligand)
>>> name 24 Ligand
>> This should do the work right ?
>>
>> On Tue, Apr 3, 2018 at 3:07 PM, Joe Jordan <e.jjordan12 at gmail.com> wrote:
>>
>>> I got a group with the right number of atoms when I tried it. What
>> version
>>> of gromacs are you using and what selection string are you using?
>>>
>>> On Tue, Apr 3, 2018 at 11:32 AM, abhisek Mondal <abhisek.mndl at gmail.com>
>>> wrote:
>>>
>>>> Location of the files:
>>>> https://drive.google.com/drive/u/0/folders/0B6O-
>>>> L5Y7BiGJfmQ4N2FpblBEcFNxaDZnaGpsUFFEUlotVWFjajR0UFFHNk5aYlhoSHVTWkU
>>>>
>>>> On Tue, Apr 3, 2018 at 2:53 PM, Joe Jordan <e.jjordan12 at gmail.com>
>>> wrote:
>>>>> Can you post the gro file and the resulting index file?
>>>>>
>>>>> On Tue, Apr 3, 2018 at 11:20 AM, abhisek Mondal <
>>> abhisek.mndl at gmail.com>
>>>>> wrote:
>>>>>
>>>>>> Hi,
>>>>>>
>>>>>> I'm just having some issue creating index file for umbrella
>> sampling.
>>>>>> I have a ligand:
>>>>>> Group    20 (NAP) has    73 elements
>>>>>>
>>>>>> Now when I run following command:
>>>>>> gmx make_ndx -f npt.gro
>>>>>>
>>>>>> and try to add NAP for index.ndx, only 6 elements were being added.
>>>>>>
>>>>>> I don't understand the problem here.
>>>>>>
>>>>>> NAP is clearly showing is of 73 elements, but how come it is
>> showing
>>>> me 6
>>>>>> elements when added to index file ?
>>>>>>
>>>>>> Please help me out here.
>>>>>>
>>>>>> Thanks.
>>>>>>
>>>>>> --
>>>>>> Abhisek Mondal
>>>>>>
>>>>>> *Senior Research Fellow*
>>>>>>
>>>>>> *Structural Biology and Bioinformatics Division*
>>>>>> *CSIR-Indian Institute of Chemical Biology*
>>>>>>
>>>>>> *Kolkata 700032*
>>>>>>
>>>>>> *INDIA*
>>>>>> --
>>>>>> Gromacs Users mailing list
>>>>>>
>>>>>> * Please search the archive at http://www.gromacs.org/
>>>>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>>>>
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>>>>>>
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>>> or
>>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Joe Jordan
>>>>> --
>>>>> Gromacs Users mailing list
>>>>>
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>> or
>>>>> send a mail to gmx-users-request at gromacs.org.
>>>>>
>>>>
>>>>
>>>> --
>>>> Abhisek Mondal
>>>>
>>>> *Senior Research Fellow*
>>>>
>>>> *Structural Biology and Bioinformatics Division*
>>>> *CSIR-Indian Institute of Chemical Biology*
>>>>
>>>> *Kolkata 700032*
>>>>
>>>> *INDIA*
>>>> --
>>>> Gromacs Users mailing list
>>>>
>>>> * Please search the archive at http://www.gromacs.org/
>>>> Support/Mailing_Lists/GMX-Users_List before posting!
>>>>
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>>>>
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>>>> send a mail to gmx-users-request at gromacs.org.
>>>>
>>>
>>>
>>> --
>>> Joe Jordan
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at http://www.gromacs.org/
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>>>
>>
>>
>> --
>> Abhisek Mondal
>>
>> *Senior Research Fellow*
>>
>> *Structural Biology and Bioinformatics Division*
>> *CSIR-Indian Institute of Chemical Biology*
>>
>> *Kolkata 700032*
>>
>> *INDIA*
>> --
>> 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
>>
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>> send a mail to gmx-users-request at gromacs.org.
>>
>
>

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

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

303 Engel Hall
340 West Campus Dr.
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