[gmx-users] Re: making index file

Vitaly Chaban vvchaban at gmail.com
Thu Aug 26 19:04:47 CEST 2010

Moedd -

Why don't you like interactive commands of make_ndx? It is easy to
form any atom groups based on your GRO file content...


Dr. Vitaly V. Chaban
Department of Chemistry
University of Rochester,
Rochester, NY, U.S.A.

>> Please let me explain my naive procedure to make index file so that you can make comment. I have created the top file for a single solvent molecule. Then removed [system] , [molecule] directives as well as "#ffgmx.itp". The [molecule type] is named 'solvent''. I got a sample itp file from a tutorial and then copied the contents of this modified top file into the file with itp extention and named it solvent.itp. Then I # included this itp file in solute. top file and based on  solvated gro file added "solvent 1000" in [molecule] directive of solute.top. solvated gro contains residues a,b,c for solute and 'SOL' for the solvent.
> That all sounds quite sensible, assuming your solvent is not water.
>> then I issue the command : make_ndx -f solvated.gro -o solvated.ndx which lists the residues :
>  >
>> 0 System              : 30350 atoms
>>   1 a                :    10 atoms
>>   2 b                 :   330 atoms
>>   3 c              :     10 atoms
>>   4 SOL                 : 30000 atoms
>> I am not getting my default groups according to [moleculetype]. Am I missing sth?  That I am only getting system index group is becase I am only using user defined residues?
> The default index groups rely on the residue names being looked up in a database of residue types (IIRC in share/top/aminoacids.dat). You'd have to tweak that for it to work in your case.

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