[gmx-users] problem with gmx genconf?

[Justin Lemkul]

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<snip>

> [ atoms ]
> ;   nr       type  resnr residue  atom   cgnr     charge       mass  typeB    chargeB      massB
> ; residue 903 DOX rtp DOX  q -0.5
>      1        CH2    903    DOX     CA      1      0.071     14.027   ; qtot 0.071
>      2        CH2    903    DOX     CB      1      0.071     14.027   ; qtot 0.142
>      3        CH2    903    DOX     CD      1      0.071     14.027   ; qtot 0.213
>      4        CH2    903    DOX     CE      1      0.071     14.027   ; qtot 0.284
>      5         OA    903    DOX     OF      1     -0.375    15.9994   ; qtot -0.091
>      6         OA    903    DOX     OG      1     -0.375    15.9994   ; qtot -0.466

This topology is complete nonsense.  You have a net charge of -0.466.  I don't 
know where you got those charges, but they make no sense whatsoever.

-Justin

>
> [ bonds ]
> ;  ai    aj funct            c0            c1            c2            c3
>     1     2     2    gb_14
>     1     6     2    gb_12
>     2     5     2    gb_12
>     3     4     2    gb_14
>     3     5     2    gb_12
>     4     6     2    gb_12
>
> [ pairs ]
> ;  ai    aj funct            c0            c1            c2            c3
>     1     3     1
>     2     4     1
>     5     6     1
>
> [ angles ]
> ;  ai    aj    ak funct            c0            c1            c2            c3
>     2     1     6     2    ga_14
>     1     2     5     2    ga_14
>     4     3     5     2    ga_14
>     3     4     6     2    ga_14
>     2     5     3     2    ga_9
>     1     6     4     2    ga_9
>
> [ dihedrals ]
> ;  ai    aj    ak    al funct            c0            c1            c2            c3            c4            c5
>     6     1     2     5     1    gd_1
>     2     1     6     4     1    gd_2
>     1     2     5     3     1    gd_2
>     5     3     4     6     1    gd_1
>     4     3     5     2     1    gd_2
>     3     4     6     1     1    gd_2
>
> ; Include Position restraint file
> #ifdef POSRES
> #include "posre.itp"
> #endif
>
> ; Include water topology
> #include "gromos43a1.ff/spce.itp"
>
> #ifdef POSRES_WATER
> ; Position restraint for each water oxygen
> [ position_restraints ]
> ;  i funct       fcx        fcy        fcz
>    1    1       1000       1000       1000
> #endif
>
> ; Include topology for ions
> #include "gromos43a1.ff/ions.itp"
>
> [ system ]
> ; Name
> DIOXANE
>
> [ molecules ]
> ; Compound        #mols
> DOX              1--------------------------------------------------------------------------------------------------------
> But, when I use the gmx genconf command to expand it into a collection of molecules (8 x 8 x 8 box), the result contains disordered molecules as seen in my VMD window. However, the .gro file produced after the genconf seems to be looking fine though. The genconf generated system looks like this:
> Screenshot from 2016-10-10 05-12-09.png
> As you can see, the molecules are not seen correctly, that is, there are many places where I have an oxygen in the place of carbon, vice-versa, only carbon containing rings, so on and so forth. Can you please let me know what's going on? I mean, there's no reason why gmx genconf shouldn't be just duplicating the molecule I give it.
>
> The command I used:
> gmx genconf -f dioxane.gro -o diox.gro -nbox 8 8 8 -dist 0.3  -shuffle -rot
>
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> Screenshot from 2016-10-10 05-12-09.png
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> Thanks & regards,Thejus Kartha
>

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

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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