[gmx-users] index file

[lina]

2011/5/12 Justin A. Lemkul <jalemkul at vt.edu>:
>
>
> lina wrote:
>>
>> make_ndx -f your.gro/pdb -n your.ndx -o your.ndx
>>
>> LiGA & LİGB:
>
> This is not correct.  You need to use | rather than &.  Using logical and
> (&) means the index group will contain atoms that are common to both LIGA
> and LIGB.  If they are distinct entities, the group will be empty.  Logical
> or (|) says merge the two different groups to create one unified group.

Ooops


>
> -Justin
>
>> q
>>
>> in grompp add -n your.ndx
>>
>>
>> 2011/5/12 ahmet yıldırım <ahmedo047 at gmail.com>:
>>>
>>> Dear users,
>>>
>>> I have two ligands. I created a special index group that merges the
>>> protein,
>>> LiGA and LİGB.
>>>
>>> I have the pr.mdp file as the following:
>>> ...
>>> energygrps      = Protein    LİGA_LİGB
>>> tc-grps         = Protein_LİGA_LİGB    Water_and_ions
>>> ...
>>>
>>> grompp -f pr.mdp -p topol.top -c em.gro -n index.ndx -o pr.tpr
>>> Fatal error:
>>> Group LİGA_LİGB not found in indexfile.
>>>
>>> I get the fatal error since I dont have a special index group that merges
>>> LiGA and LİGB. should I create two different index file?
>>>
>>> Thanks in advance
>>> --
>>> Ahmet YILDIRIM
>>>
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>>
>>
>>
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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-- 
Best Regards,

lina