|
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
-----------------------------------------
Marino Convertino Dept. Farmaco Chimico University of Bari |
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