VMD-L Mailing List

From: Arneh Babakhani (ababakha_at_mccammon.ucsd.edu)
Date: Wed Aug 15 2007 - 13:06:17 CDT

I see, ok, thanks for the clarification (I didn't know the index keyword
was internal),

appreciate the help,

Arneh

Peter Freddolino wrote:
> Hi Arneh,
> in VMD, the "index" keyword is defined internally, not by the input
> file, and is always a zero-indexed list of the atoms. If you want a
> 1-indexed list instead, try using the "serial" keyword instead.
> Peter
>
> Arneh Babakhani wrote:
>
>> Hi
>>
>> I noticed that gro files (structure files from GROMACS) start with an
>> atom index = 1. When you read in the gro file, vmd sets the indices
>> back one, so the atom in the gro file with index=1 is now index = 0.
>>
>> Case in point (an excerpt from the gro file):
>> Protein in water
>> 99776
>> 1GLN N 1 4.241 3.617 2.284 -0.6878 0.3661 -0.3811
>>
>>
>> in the vmd tcl console:
>> % set temp [atomselect top "index 0"]
>> $temp get name
>> N
>> $temp set index 1
>> atomsel object: set: data not modifiable: index
>>
>>
>> My question is, how do you change the index values so they can match
>> what's in the gro file? (This is important if you want to make
>> atomselections, to define groups, to be used later with the GROMACS
>> analysis scripts).
>>
>> Thanks,
>>
>> Arneh
>>
>
>