Hi,
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.
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
Fatal error:
Atoms in the .top are not numbered consecutively from 1
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.
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.
I post here the whole error message, hoping that it can be useful.
Option Filename Type Description
------------------------------------------------------------
-pfg dynamin_dimer_fg.top Input Topology file
-pcg dynamin_dimer_cg.top Input, Opt! Topology file
-c dyn_dimer_cg.gro Input Generic trajectory: xtc trr trj gro g96
pdb
-o dynamin_dimer_fg_random.groq.gro Output Generic structure: gro
g96 pdb xml
Option Type Value Description
------------------------------------------------------
-[no]h bool no Print help info and quit
-nice int 0 Set the nicelevel
-n int 0 1: fg2cg transformation, 0: cg2fg transformation
-wat int 0 1: rewrites FG_CG water to true fg water;
-rad real 0.3 A radius for random atom insertion;
calling cpp...
dynamin_dimer_fg.top:38:2: error: invalid preprocessing directive #;
dynamin_dimer_fg.top:51:2: error: invalid preprocessing directive #SOL
cpp exit code: 256
Tried to execute: 'cpp
-I/home/cocktail/vitalini/GROMACS_Tutorial/cg_aa_prova/cg_aa_dynamin_dimer/prova2/../../../../gromacs_special/share/gromacs/top
dynamin_dimer_fg.top > gromppqBsIeH'
The 'cpp' command is defined in the .mdp file
processing topology...
Generated 165 of the 1596 non-bonded parameter combinations
Cleaning up temporary file gromppqBsIeH
-------------------------------------------------------
Program g_fg2cg, VERSION 3.3.1
Source code file: ../kernel/toppush.c, line: 758
Fatal error:
Atoms in the .top are not numbered consecutively from 1
Hope you can help me with that.
Many Thanks
Francesca
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
