[gmx-users] complex topology nr error

Justin Lemkul jalemkul at vt.edu
Sun Feb 28 15:18:33 CET 2016

On 2/28/16 5:48 AM, Sana Saeed wrote:
> [history: i am working on ligand protein complex to find out free binding
> energy. i amde complex topology, and you suggested that i should put my
> distance restraints directive after molcules directive, when i did so it gave
> me error about atom 2023 out of range (2023 is my ligand atom, but in
> topology it is atom number 3. then i changed the directives places like
> mentioned following:1.   #include ff2.    [moleculetype]      protein
> ligand 3.   protein topogy contents4.   #include "ligand.itp5.   [distance
> restraints6.    [angle restraints]7.    [dihedral restraints]8.    Position
> restraint complex9. water topology and restraints10. ions topology11.
> [system]12. [molecules]i got this errorAtoms in the .top are not numbered
> consecutively from 1 (rather, atomnr = 1, while at->nr = 2121) : this is
> because in the topology file 2121 is SOL (water molecule) what should i do
> now.

I've already told you what to do a couple of times and even provided you with a 
framework of the topology yesterday.  You're still making no mention of the 
crucial directive that you need: [intermolecular_interactions].

If you want free help, follow what you've been told and ask new questions based 
on what happens then.  It's not productive for either of us for me to keep 
repeating the same thing and for you to keep on not following it.



Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441


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