[gmx-users] (no subject)

[Justin Lemkul]

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.

This mailing list does not accept attachments. If you need to share 
files, use a file-sharing service and provide the URL.

-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

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

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