[gmx-users] (no subject)

maya nair mayasnair1 at gmail.com
Fri Nov 23 07:01:13 CET 2018

I am trying to do the molecular dynamics of  DNA-ligand complex. I made the
ligand files using antechamber and converted the amber files to .gro and
.top using acpype.pl. Then I made the complex.gro. when I am trying to run
grommp  ions.mdp and em.mdp, it gives error saying the following

Command line:
  gmx grompp -f ions.mdp -c solv.gro -p topol1.top -o ions.tpr

Back Off! I just backed up mdout.mdp to ./#mdout.mdp.20#
Setting the LD random seed to 2988957772

WARNING 1 [file res.itp, line 5]:
  Too few gb parameters for type 1

Couldn't find topology match for atomtype 1
Aborted (core dumped)

I couldnot understand about the atomtype. I checked in the .atp file and
found that nomenclatures exist there. So couldnot do any rectification.
Help me in this regard. I am attaching my files.
Thank you

[image: Attachments]

Maya S Nair
Assistant Professor
Department of Biotechnology
IIT Roorkee

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