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<DIV><FONT face=Arial size=2>Dear all,</FONT></DIV>
<DIV><FONT face=Arial size=2>sorry for the long message.</FONT></DIV>
<DIV>
<DIV><FONT face=Arial size=2>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.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>In order to allow them to interact I am using
pull code.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>My pull.ppa is as follows:</FONT></DIV>
<DIV><FONT face=Arial
size=2>verbose
= no</FONT></DIV>
<DIV><FONT face=Arial
size=2>runtype
= afm</FONT></DIV>
<DIV><FONT face=Arial
size=2>group_1 =
p2 ;protein_2 residues 43-84</FONT></DIV>
<DIV><FONT face=Arial
size=2>reference_group = p1 ;
protein_1 residues 1-42</FONT></DIV>
<DIV><FONT face=Arial
size=2>reftype =
com_t0</FONT></DIV>
<DIV><FONT face=Arial size=2>reflag
=
1</FONT></DIV>
<DIV><FONT face=Arial size=2>pulldim
= Y Y
Y</FONT></DIV>
<DIV><FONT face=Arial
size=2>afm_rate1 =
0.025 </FONT></DIV>
<DIV><FONT face=Arial
size=2>afm_k1 =
1000</FONT></DIV>
<DIV><FONT face=Arial
size=2>afm_init1 =
0.0 0.0 0.0</FONT></DIV>
<DIV><FONT face=Arial
size=2>afm_dir1 =
0.0 0.0 0.1</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>I am giving the following
commands:</FONT></DIV>
<DIV><FONT face=Arial size=2>>grompp -f PME_NPT_fullMD.mdp -c Pull_2_eql.gro
-p Pull.top -o Pull_fullMD.tpr -v</FONT></DIV>
<DIV><FONT face=Arial size=2>>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 &</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Unfortunately, the calculation does not start and
checking the fullMD.log I have returned as follows:</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Program mdrun, VERSION 3.3_beta_20050202<BR>Source
code file: pullinit.c, line: 215</FONT></DIV></DIV>
<DIV><FONT face=Arial size=2>Fatal error:<BR> in the index file2<BR>Halting
program mdrun</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>I think that the file2 means 'file p2' (the group_1
in the Pull.ppa, infact changing that name, also the error change
accordingly)</FONT></DIV>
<DIV><FONT face=Arial size=2>Can anyone help me?</FONT></DIV>
<DIV><FONT face=Arial size=2>What can I do in order to solve this
problem?</FONT></DIV>
<DIV><FONT face=Arial size=2>Thanks in advance.</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>Marino</FONT></DIV>
<DIV><FONT face=Arial size=2></FONT> </DIV>
<DIV><FONT face=Arial size=2>-----------------------------------------<BR>Marino
Convertino<BR>Dept. Farmaco Chimico<BR>University of
Bari<BR></FONT></DIV></BODY></HTML>