[gmx-users] nvt equilibration; error

[Ray, Bruce D]

On Jun 4, 2015, at 11:15 PM, <gromacs.org_gmx-users-request at maillist.sys.kth.se>
 <gromacs.org_gmx-users-request at maillist.sys.kth.se> wrote:

> Date: Thu, 4 Jun 2015 20:15:54 -0700
> From: marzieh dehghan <dehghanmarzieh at gmail.com>
> To: gromacs.org_gmx-users at maillist.sys.kth.se
> Subject: [gmx-users] nvt equilibration; error
> Message-ID:
> 	<CA+6Z3Gn7egqGXnox9n3fD9Kk0+DKZT6Leo60a=LZG2_p7-3BrQ at mail.gmail.com>
> Content-Type: text/plain; charset=UTF-8
> 
> Hi
> Dear Justin
> 
> thanks a lot for your kind answer
> 
> after creating a topology file using topolbuild, all parameters such as
> information about bond, angle, . . . were completed based on ffbond.itp.
> then I used topol file to held energy minimization by gromacs and after
> holding NVT command, I confronted to the mentioned error
> 
> "Group Protein not found in index file"
> 
> 
> I would like to know, this method is correct?
> 
> thank you
> 
> best wishes

I cannot tell from this why you would expect a group called Protein
in your topology.  If you do not have a group named Protein in the
topology, then any reference to such a group requires that it be
defined in an index file.

What was the name in the mol2 file for the compound for which you
generated the topology?  What does the topology call the molecule?
I think that you should use that group name rather than Protein
as a group name in the *.md you feed to grompp


-- 
Bruce D. Ray, Ph.D.
Associate Scientist
IUPUI
Physics Dept.
402 N. Blackford St., Rm. LD-061
Indianapolis, IN  46202