[gmx-users] Error in grompp for protein-ligand tutorial

[Justin Lemkul]

On 1/28/14, 1:28 PM, José Adriano da Silva wrote:
> Thanks Justin, I appreciate you checked the topology file that has these
> problems. Because I repeated several times the sequence of steps with different
> complex and presents the same error.
>

This is your problem:

[ moleculetype ]
; Name            nrexcl
Protein_chain_A     3

[ moleculetype ]
; Name            nrexcl
JZ4                 1

You're defining a protein moleculetype with nothing in it, then for some reason 
defining a JZ4 (the ligand in the tutorial) moleculetype, but its atoms are the 
protein.

Rule of thumb - Don't add or modify moleculetypes in the .top, just #include new 
molecules.

-Justin

> attached file
>
>
> 2014-01-28 Justin Lemkul <jalemkul at vt.edu <mailto:jalemkul at vt.edu>>
>
>
>
>     On 1/27/14, 2:15 PM, José Adriano da Silva wrote:
>
>            I am new to Gromacs, then follow the tutorial protein-ligand, decided to
>         adapt the procedure for my protein (acetylcholinesterase) and my binder. The
>         procedure is this (protein-ligand complex):
>
>
>
>
>         <http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin/__gmx-tutorials/comp
>         <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/comp>
>         lex/index.html>
>         http://www.bevanlab.biochem.__vt.edu/Pages/Personal/justin/__gmx-tutorials/compl
>         <http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/compl>
>         ex/index.html
>
>
>
>
>         Well, I switched to facilitate the name of my protein and my binder by the
>         names used in the tutorial. The problem occurs when I do the command:
>
>
>
>         grompp -f em.mdp -c solv.gro -p topol.top -o ions.tpr
>
>
>
>
>
>         The following error occurs:
>
>
>
>         Fatal error:
>
>         Molecule type 'Protein_chain_A' contains no atoms
>
>
>     The error suggests that the topology is probably empty, which you can
>     inspect with a text editor.  Maybe pdb2gmx failed, but the fatal error from
>     that step should have been quite obvious.  Otherwise, some modification that
>     you have made to the topology has rendered its format unintelligible.
>
>     -Justin
>
>     --
>     ==============================__====================
>
>     Justin A. Lemkul, Ph.D.
>     Postdoctoral Fellow
>
>     Department of Pharmaceutical Sciences
>     School of Pharmacy
>     Health Sciences Facility II, Room 601
>     University of Maryland, Baltimore
>     20 Penn St.
>     Baltimore, MD 21201
>
>     jalemkul at outerbanks.umaryland.__edu
>     <mailto:jalemkul at outerbanks.umaryland.edu> | (410) 706-7441
>     <tel:%28410%29%20706-7441>
>
>     ==============================__====================
>     --
>     Gromacs Users mailing list
>
>     * Please search the archive at
>     http://www.gromacs.org/__Support/Mailing_Lists/GMX-__Users_List
>     <http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List> before posting!
>
>     * Can't post? Read http://www.gromacs.org/__Support/Mailing_Lists
>     <http://www.gromacs.org/Support/Mailing_Lists>
>
>     * For (un)subscribe requests visit
>     https://maillist.sys.kth.se/__mailman/listinfo/gromacs.org___gmx-users
>     <https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users> or send
>     a mail to gmx-users-request at gromacs.org <mailto:gmx-users-request at gromacs.org>.
>
>

-- 
==================================================

Justin A. Lemkul, Ph.D.
Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

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

==================================================