On 11/23/18 12:58 AM, maya nair wrote:
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.
The .atp file is only read by pdb2gmx, so it's not relevant. Apparently you have an atom type "1" (number one) in your topology, which is very strange. It doesn't have parameters defined in gb.itp, so you get a failure. Make sure your input is sound and your topology/force field files are free of typos.
Help me in this regard. I am attaching my files.
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-Justin -- ================================================== Justin A. Lemkul, Ph.D. Assistant Professor Office: 301 Fralin Hall Lab: 303 Engel Hall Virginia Tech Department of Biochemistry 340 West Campus Dr. Blacksburg, VA 24061 jalem...@vt.edu | (540) 231-3129 http://www.thelemkullab.com ================================================== -- Gromacs Users mailing list * Please search the archive at http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before posting! * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists * For (un)subscribe requests visit https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or send a mail to gmx-users-requ...@gromacs.org.
