On 9/29/12 12:55 PM, Ali Alizadeh wrote:
Dear All users
I have a system with 3 layers,
when i run grompp program, encounter with this error.
First and 3th layer is the same, and middle layer is water. what's
this error about?
grompp is looking for some group called "1" (the number one) but it can't find
such a group. The error suggests that you use a custom index group. In the
absence of an .mdp file and a list of the index groups that you're trying to
use, we can't really guess what's supposed to be happening.
and i have another question about make_ndx, How to make index the same
atoms with different res number in .gro file?
Type "help" at the make_ndx prompt to see examples. If you need specific help
with a specific task, ask a more specific question :)
-Justin
..........................................
Ignoring obsolete mdp entry 'title'
Ignoring obsolete mdp entry 'cpp'
Ignoring obsolete mdp entry 'nstcheckpoint'
Back Off! I just backed up mdout.mdp to ./#mdout.mdp.7#
Generated 332520 of the 332520 non-bonded parameter combinations
Generating 1-4 interactions: fudge = 0.5
Generated 332520 of the 332520 1-4 parameter combinations
Excluding 3 bonded neighbours molecule type 'Ion'
turning all bonds into constraints...
Excluding 3 bonded neighbours molecule type 'Ion2'
turning all bonds into constraints...
Excluding 2 bonded neighbours molecule type 'SOL'
turning all bonds into constraints...
Analysing residue names:
There are: 1183 Ion residues
There are: 1830 Water residues
Analysing residues not classified as Protein/DNA/RNA/Water and
splitting into groups...
Number of degrees of freedom in T-Coupling group System is 23990.00
-------------------------------------------------------
Program grompp, VERSION 4.5.5
Source code file: /build/buildd/gromacs-4.5.5/src/kernel/readir.c, line: 1320
Fatal error:
Group 1 not found in index file.
Group names must match either [moleculetype] names
or custom index group names,in which case you
must supply an index file to the '-n' option of grompp.
--
========================================
Justin A. Lemkul, Ph.D.
Research Scientist
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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