[gmx-users] Position restraints

Justin Lemkul jalemkul at vt.edu
Fri Mar 14 21:39:28 CET 2014

On 3/14/14, 4:28 PM, Nimmy McNimmerson wrote:
> I have a .top file looking like this:
> #include "spc.itp"
> #include "ffgmx.itp"
> #include "lipid.itp"
> #define POSRES_LIPID
> #include "mylipid.itp"
> #include "dppc.itp"
> [ system ]
> test system
> [ molecules ]
> ; Compound        #mols
> DX5                 200
> DPPC        200
> The #define POSRES_LIPID is used to determine whether to include position restraints in mylipid.itp. However, when I try to run grompp on this (with everything the exact same as before I included the position restraints), I get the error "Topology include file "lipid_posre.itp" not found". If I take out all the position restraints, it works fine and grompp does what is expected. What's going on? I never asked to include this file, I don't even know what lipid_posre.itp is and google has no results on it. I tried adding #include "lipid_posre.itp" at the top of the .top file, just to see what happened, but I got the same error. How am I supposed to add position restraints? The GROMACS manual just says to add them and doesn't mention additional includes, and I added them in the same way that the manual said to.

You did ask to #include the position restraints because you're explicitly using 
#define to set the inclusion conditions to be true.

If you don't know what's calling "lipid_posre.itp," that's what grep is for. 
It's probably dppc.itp, which includes the option to restrain the lipids under a 
conditional #ifdef POSRES_LIPID.  Your topology says "turn on lipid restraints," 
and one of the lipid .itp files (again, probably dppc.itp) says "if lipid 
restraints are turned on, #include "lipid_posre.itp."

Remove the #define statement from the topology; that's not normal use 
(technically correct in terms of syntax, but then it's always true, which is 
probably not what you want) and instead use "define -DPOSRES_LIPID" in the .mdp 
file to conditionally trigger the restraints.



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


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