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<p class="MsoNormal"><span lang="EN-US">Hi,</span></p>
<p class="MsoNormal"><span lang="EN-US">I'm a new GROMACS user and I'm trying to
convert a CG file (I have the .top and .gro for it) to AA using the reverse
command g_fg2cg.</span></p>
<p class="MsoNormal"><span lang="EN-US">Unfortunately I don't have the AA topology
file, only the pdb, so I'm trying to get one using pdb2gmx genbox and genion
subsequently. Then I try to run the g_fg2cg command and what I get is an error
message </span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US">Fatal error:</span></p>
<p class="MsoNormal"><span lang="EN-US">Atoms in the .top are not numbered
consecutively from 1</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US">I have checked the FG .top file and
actually found that the residues were not named from one, so I changed it and
tried again but with the same result. In my system I have a dimer plus water
plus ions so I thought that the problem might have occurred because in the .itp
files for each monomer the residue numeration was starting from 1; not knowing
if it could cause the problem I tried to re-numerate the residues in the second
.itp file in order to match with those of the first file but with no change in
the result.</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US">I’ve read on the web that with grompp a
similar error message was found and it was due to the presence of ions after
solvent so I tried to change the order of the ion.itp file in the topology but
it didn’t change anything.</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US">I post here the whole error message, hoping
that it can be useful. </span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US">Option<span style> </span>Filename<span style> </span>Type<span style> </span>Description</span></p>
<p class="MsoNormal"><span lang="EN-US">------------------------------------------------------------</span></p>
<p class="MsoNormal"><span lang="EN-US">-pfg dynamin_dimer_fg.top<span style> </span>Input<span style> </span>Topology file</span></p>
<p class="MsoNormal"><span lang="EN-US">-pcg dynamin_dimer_cg.top<span style> </span>Input, Opt!<span style> </span>Topology file</span></p>
<p class="MsoNormal"><span lang="EN-US"><span style>
</span>-c dyn_dimer_cg.gro<span style>
</span>Input<span style> </span>Generic trajectory: xtc
trr trj gro g96</span></p>
<p class="MsoNormal"><span lang="EN-US"><span style>
</span><span style> </span>pdb</span></p>
<p class="MsoNormal"><span lang="EN-US"><span style>
</span>-o dynamin_dimer_fg_random.groq.gro<span style> </span>Output<span style> </span>Generic structure: gro</span></p>
<p class="MsoNormal"><span lang="EN-US"><span style>
</span>g96 pdb xml</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US"><span style> </span>Option<span style> </span>Type<span style>
</span>Value<span style> </span>Description</span></p>
<p class="MsoNormal"><span lang="EN-US">------------------------------------------------------</span></p>
<p class="MsoNormal"><span lang="EN-US"><span style> </span>-[no]h<span style> </span>bool<span style> </span>no<span style>
</span>Print help info and quit</span></p>
<p class="MsoNormal"><span lang="EN-US"><span style> </span>-nice<span style> </span>int<span style> </span>0<span style> </span>Set the nicelevel</span></p>
<p class="MsoNormal"><span lang="EN-US"><span style> </span>-n<span style> </span>int<span style> </span>0<span style> </span>1: fg2cg transformation, 0: cg2fg
transformation</span></p>
<p class="MsoNormal"><span lang="EN-US"><span style> </span>-wat<span style> </span>int<span style> </span>0<span style> </span>1: rewrites FG_CG water to true fg
water; </span></p>
<p class="MsoNormal"><span lang="EN-US"><span style> </span>-rad<span style> </span>real<span style> </span><span style> </span>0.3<span style> </span>A radius for random atom insertion; </span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US">calling cpp...</span></p>
<p class="MsoNormal"><span lang="EN-US">dynamin_dimer_fg.top:38:2: error: invalid
preprocessing directive #;</span></p>
<p class="MsoNormal"><span lang="EN-US">dynamin_dimer_fg.top:51:2: error: invalid
preprocessing directive #SOL</span></p>
<p class="MsoNormal"><span lang="EN-US">cpp exit code: 256</span></p>
<p class="MsoNormal"><span lang="EN-US">Tried to execute: 'cpp<span style> </span>-I/home/cocktail/vitalini/GROMACS_Tutorial/cg_aa_prova/cg_aa_dynamin_dimer/prova2/../../../../gromacs_special/share/gromacs/top<span style> </span>dynamin_dimer_fg.top > gromppqBsIeH'</span></p>
<p class="MsoNormal"><span lang="EN-US">The 'cpp' command is defined in the .mdp
file</span></p>
<p class="MsoNormal"><span lang="EN-US">processing topology...</span></p>
<p class="MsoNormal"><span lang="EN-US">Generated 165 of the 1596 non-bonded
parameter combinations</span></p>
<p class="MsoNormal"><span lang="EN-US">Cleaning up temporary file gromppqBsIeH</span></p>
<p class="MsoNormal"><span lang="EN-US">-------------------------------------------------------</span></p>
<p class="MsoNormal"><span lang="EN-US">Program g_fg2cg, VERSION 3.3.1</span></p>
<p class="MsoNormal"><span lang="EN-US">Source code file: ../kernel/toppush.c,
line: 758</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US">Fatal error:</span></p>
<p class="MsoNormal"><span lang="EN-US">Atoms in the .top are not numbered consecutively
from 1</span></p>
<p class="MsoNormal"><span lang="EN-US"> </span></p>
<p class="MsoNormal"><span lang="EN-US">Hope you can help me with that.</span></p>
<p class="MsoNormal"><span lang="EN-US">Many Thanks</span></p>
<p class="MsoNormal"><span lang="EN-US">Francesca</span></p>