[gmx-users] pull code bug?

Marino Convertino convertino at farmchim.uniba.it
Mon Mar 20 17:59:34 CET 2006

Dear all,
sorry for the long message.
I am simulating the hydrophobic interaction between two 42-aminoacid oligopeptides in pbc conditions with acqueous explicit solvent with all-bonds constraints (LINCS) by GROMACS 3.3 downloaded from GROMACS web-site.

In order to allow them to interact I am using pull code.

My pull.ppa is as follows:
verbose                  =   no
runtype                  =   afm
group_1                 =   p2 ;protein_2 residues 43-84
reference_group      =   p1 ; protein_1 residues 1-42
reftype                   =   com_t0
reflag                     =   1
pulldim                   =   Y Y Y
afm_rate1               =   0.025 
afm_k1                   =   1000
afm_init1                 =   0.0  0.0  0.0
afm_dir1                  =   0.0  0.0  0.1

I am giving the following commands:
>grompp -f PME_NPT_fullMD.mdp -c Pull_2_eql.gro -p Pull.top -o Pull_fullMD.tpr -v
>mdrun -s Pull_fullMD.tpr -o Pull_fullMD.trr -c Pull_fullMD.gro -e Pull_fullMD.edr -pi pull.ppa -pn pull.ndx -po -pdo -v > & fullMD.log &

Unfortunately, the calculation does not start and checking the fullMD.log I have returned as follows:

Program mdrun, VERSION 3.3_beta_20050202
Source code file: pullinit.c, line: 215
Fatal error:
 in the index file2
Halting program mdrun

I think that the file2 means 'file p2' (the group_1 in the Pull.ppa, infact changing that name, also the error change accordingly)
Can anyone help me?
What can I do in order to solve this problem?
Thanks in advance.


Marino Convertino
Dept. Farmaco Chimico
University of Bari
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