Re: [gmx-users] Group protein not found in indexfile

2013-11-06 Thread Justin Lemkul
On 11/6/13 1:52 PM, Steve Seibold wrote: Hello I am having trouble running a dimmer invacuo simulation. I can do energy minimization on it, but when I attempt to generate md.tpr file I get this weird message about “Group Protein not found in index”. I don’t see why I would need an index file.

Re: [gmx-users] Group protein not found in indexfile

2013-11-04 Thread Justin Lemkul
On 11/4/13 3:03 PM, Steve Seibold wrote: Hi Justin Thanks for your response. Here are the files you asked for. They are all text files. I am still attempting to fix this, but am still getting the error I described no matter what I have done so far. The list does not accept attachments, nor

Re: [gmx-users] Group protein not found in indexfile

2013-11-04 Thread Justin Lemkul
On 11/4/13 1:29 PM, Steve Seibold wrote: Hello I am just trying to do a simple MD on a dimmer system (in which the dimmers are NOT identical). I can use pdb2gmx to create a topology file and four .itp files pores.chainA.itp, pores.chainX.itp; system.Protein.chainA.itp and system.Protein.