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

[Vitaly Chaban]

Hey -

I need to see"rrg.itp" and "drg.itp" to undesrtand the situation.

=============================================================================
* Dr. Vitaly V. Chaban         |  skype: vvchaban                           *
* Department of Chemistry      |  email: v.chaban at rochester.edu             *
* University of Rochester      |  email: vvchaban at gmail.com                 *
* Rochester, NY 14627-0216     |  Tel.: 585-276-5751                        *
* United States of America     |  WWW: chem.rochester.edu/~prezhdo_group/   *
=============================================================================





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.

                              Please help me to find out the problem.

---------------------
HARESH AJANI
09377756124
ajani_haresh at yahoo.co.in