[gmx-users] Re: "moleculetype DRG is redefined"

[Justin A. Lemkul]

Please keep all Gromacs-related correspondence on the gmx-users list.  I am not
a private help service.  I have CC'ed this message to the list and I would ask
that all further correspondence be sent to the list.  See comments below.

Quoting AJANI HARESH <ajani_haresh at yahoo.co.in>:

> Respected Sir,
>
>
> I am HARESH AJANI from CADILA HEALTHCARE LTD, INDIA.
>
> I am using gromacs at my Department of Bioinformatics.
>
> I am going to simulate an enzyme complex taking a ligand at active site and
> another ligand at allosteric site.
>
> When I ran md simulation taking ligand at active site only then it was ok.
> But when I am running the simulation taking both they show "moleculetype DRG
> is redefined"
>
>
> my topolgy  look like this
> >                              #include "ffG43a1.itp"
> >                              #include "rrg.itp"
> >                              #include "drg.itp"
> >                          and at the end it is like this
> >
> >                                         Protein             1
> >                                         RRG                 1
> >                                         DRG                 1
>                                           SOL                10
> >                                         SOL             17662
>
>
>
> I can not understand why GROMACS takes into account bcause they are far apart
> or is there any wrong to my pdb file. I am genereting the coordinate and
> topology using PRODRG server.
>

The problem has nothing to do with your coordinate file.  PRODRG, by default,
names all of its [moleculetypes] "DRG," so you need to assign a proper name in
this directive.  Presumably, you want one of them to be RRG, but it is not set
as such in rrg.itp.

As always, beware the quality of PRODRG topologies:

http://www.gromacs.org/Downloads/Related_Software/PRODRG#Tips

-Justin

>                               Please help me to find out the problem.
>
> ---------------------
> HARESH AJANI
> 09377756124
> ajani_haresh at yahoo.co.in
>
>
>


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

Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

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