[gmx-users] two ligand itp file from ACPYPE

SEMRAN İPEK semranipek at gmail.com
Wed Feb 19 15:44:19 CET 2014

Dear Users;

Iwould like to run MD calculations using gromacs 4.6.5. My topology file
has two ligand. The itp files for these ligands have been generated using
*I have followed the instructions given below to  include
these separate itp files to the topology file. For instance, atomtypes.itp
file includes only common atomtypes for two ligands. ligan1.itp and
ligand2.itp files have their own parameters and starts with *

*[ moleculetype ] directives.*
*BTW, the conf.gro file has been modified to reflect the changes in
topology file. Conf.gro file exactly follows the same atom order as in the
case of topology file.*
*When I try to run;*
*editconf_d -f conf.gro  -o newbox.gro -bt dodecahedron -d 1.0, **it gives
an error like this:*

 Invalid line in conf.gro for atom 1:
1 p  C6N    1   0.044   0.083  -0.081

Presumably, the problem is related to my conf.gro. Could you please shed
light on this issue? How can I include two ligand of which parameters have
been gathered from ACPYPE?

#include "amber99.ff/forcefield.itp"

; only has [atomtypes]
#include "my_ligand_atomtypes.itp"

; these don't introduce [atomtypes] any more
 #include "ligand1.itp"
#include "ligand2.itp"


Best Regards,


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