[gmx-users] Running GROMACS with DNA

[p.keymer at student.qut.edu.au]

Hi gmx-users

I am trying to analyze a protein-DNA interaction and have 
been having trouble. I am running a test on on a single 
strand of DNA .I have renamed the the nucleotides as 
suggested on this mailing list.  I manage to get as far as 
an energy minimization but when I attempt a position 
restrained mdrun I get an error from grompp.Please can 
someone help. Also can someone suggest what I can do to 
analyze my protein-DNA interaction in gromacs.

Below is the grompp output:


creating statusfile for 1 node...

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.1#
Warning: as of GMX v 2.0 unit of compressibility is truly 
1/bar
checking input for internal consistency...
calling /lib/cpp...
processing topology...
Excluding 3 bonded neighbours for Protein_A           1
turning all bonds into constraints...
Excluding 1 bonded neighbours for SOL               796
turning all bonds into constraints...
WARNING 1 [file "dna.top", line 1177]:
  System has non-zero total charge: -1.493000e+01

processing coordinates...
double-checking input for internal consistency...
Velocities were taken from a Maxwell distribution at 300 K
Reading position restraint coords from after_em.gro
renumbering atomtypes...
converting bonded parameters...
#     ANGLES:   1120
#      PDIHS:   430
#      IDIHS:   620
#       LJ14:   837
#     POSRES:   328
#     CONSTR:   549
#     SETTLE:   1592
Walking down the molecule graph to make shake-blocks
initialising group options...
processing index file...
Analysing residue names:
Opening library file /pkg/gromacs/share/top/aminoacids.dat
There are:   804      OTHER residues
There are:     0    PROTEIN residues
There are:     0        DNA residues
Analysing Other...
Fatal error: Group Protein not found in indexfile.
Maybe you have non-default goups in your mdp file, while not 
using the '-n' option of grompp.
In that case use the '-n' option.


Thanks in advance

Philip