RE: [gmx-users] error in producing top file for a structure

2012-09-08 Thread Elie M
Thanks very much for the help. I will see what I can do about that. Sincerely ELie > Date: Sat, 8 Sep 2012 16:50:00 -0400 > From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] error in producing top file for a structure > > > > On 9/8/

Re: [gmx-users] error in producing top file for a structure

2012-09-08 Thread Justin Lemkul
On 9/8/12 4:46 PM, Elie M wrote: Thanks a lot for your response. Actually i do have LIG , which obviosuly the code did not understand and changed it into LI; at first I thought LI was LIG but in GROMACS' language. Is there any place where I can read how to implement changes in the .rtp file?

RE: [gmx-users] error in producing top file for a structure

2012-09-08 Thread Elie M
From: jalem...@vt.edu > To: gmx-users@gromacs.org > Subject: Re: [gmx-users] error in producing top file for a structure > > > > On 9/8/12 4:29 PM, Elie M wrote: > > > > Dear all, > > I am new to GROMACS. I am trying to minimize a structure but first I have > &

Re: [gmx-users] error in producing top file for a structure

2012-09-08 Thread Justin Lemkul
On 9/8/12 4:29 PM, Elie M wrote: Dear all, I am new to GROMACS. I am trying to minimize a structure but first I have to form the pdb file with the correct force field parameters. I am using version 4.0.5 and an OPLSAA force field. The error I am getting is:...Opening library file /cygd