[gmx-users] flat-bottom reference file format

[Justin Lemkul]

On 3/14/16 4:20 PM, Jinmei Wang wrote:
> dear list,
>
> I want to restrain a group of atoms within one sphere. I got the sphere
> center coordinate using g_traj
>
> In topol.top I added this part:
>
> #ifdef POSRES_FLATBOTTOM
> [ position_restraints ]
> ;  i funct       g        r(nm)        k (kJ/mol/nm)
>     4    2        1        1.5          300000
>   857    2        1        1.5          300000
> 1715    2        1        1.5          300000
> #endif
>
> and in the reference file I put:
>
> ATOM      4  CA  GLY   704      21.698  27.798   9.333  1.00  0.00
>    C
> ATOM   857  CA  GLY   704      21.698  27.798   9.333  1.00  0.00
> C
> ATOM 1715  CA   GLY   704      21.698  27.798   9.333  1.00  0.00
> C
>
> but I came across this error:
>
> WARNING 1 [file topol.top, line 16661]:
>   The number of atoms in flat.pdb (3) does not match the number of atoms in
> the topology (97123). Will assume that the first 3 atoms in the topology
> and flat.pdb match.
>
> could anybody tell me what's wrong with my -r file? it goes well without
> giving reference file.
>

The coordinates passed to -r must be a complete file; you don't just pass the 
restrained coordinates (that's taken care of in the topology).

-Justin

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

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

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