[gmx-users] Position restrain Bilayer

[Justin Lemkul]

On 8/26/15 10:57 AM, khada at web.de wrote:
> Hey folks!
> I want to position restrain my lipid bilayer for minimization and
> equibriliation, but grommp gives me following error:
> Fatal error:
> [ file posresdppe.itp, line 17 ]:
> Atom index (13) in position_restraints out of bounds (1-12).
> I generated the *.itp files with genrestr -f membrane-ecoli.gro -n index.ndx -o
> posres{insert lipidname}.itp, making sure atom indices match with my index file.

genrestr can only work with a single molecule.  Note the caveat in the help 
description.  If you're feeding it something with multiple molecules, it won't 
work (OK, there are ways around that or that you can fix it afterwards, but keep 
it simple).

-Justin

> I think I've put them in the right order in the topology:
> #include "martini.itp"
> #include "martini_ions.itp"
> [ moleculetype ]
> #include "DPPE.itp"
> #ifdef POSRES_LIPID
> #include "posresdppe.itp"
> #endif
> #include "DOPE.itp"
> #ifdef POSRES_LIPID
> #include "posresdope.itp"
> #endif
> #include "POPE.itp"
> #ifdef POSRES_LIPID
> #include "posrespope.itp"
> #endif
> #include "POPG.itp"
> #ifdef POSRES_LIPID
> #include "posrespopg.itp"
> #endif
>
> [ system ]
> e coli membrane
> [ molecules ]
> DPPE            61
> DOPE            61
> POPE            61
> POPG            61
> DPPE            61
> DOPE            61
> POPE            61
> POPG            61
> W             7166
> NA+            140
> CL-             18
> So whats wrong? Do you have an idea?
> Thanks in advance! :)
> Warm regards,
> Kathrin
>
>

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

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
http://mackerell.umaryland.edu/~jalemkul

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