[gmx-users] Running GROMACS with DNA

Andrey V Golovin golovin at genebee.msu.su
Tue Jul 20 08:49:25 CEST 2004

Dear p,

Tuesday, July 20, 2004, 6:01:41 AM, you wrote:

check yours pr.mdp especially temperature coupling section or pressure
coupling. create group for in index file and check  groups in mdp file

pksqea> Hi gmx-users

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

pksqea> Below is the grompp output:

pksqea> creating statusfile for 1 node...

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

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

pksqea> Thanks in advance

pksqea> Philip
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Best regards,
 Andrey                            mailto:golovin at genebee.msu.su

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