[gmx-users] index file

[Justin A. Lemkul]

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.

-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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