Aw: [gmx-users] Re: Re: help with chromophore of a GFP

2013-03-25 Thread lloyd riggs
: Montag, 25. März 2013 um 16:56 Uhr Von: "Anna MARABOTTI" An: gmx-users@gromacs.org Betreff: [gmx-users] Re: Re: help with chromophore of a GFP Dear gmx-users, I'm still dealing with my problem of obtaining parameters for my chromophore of the GFP family, in order to treat it a

Re: [gmx-users] Re: Re: help with chromophore of a GFP

2013-03-25 Thread Mark Abraham
On Mon, Mar 25, 2013 at 4:56 PM, Anna MARABOTTI wrote: > > > Dear gmx-users, > > I'm still dealing with my problem of obtaining > parameters for my chromophore of the GFP family, in order to treat it as > a new residue. I'm trying (VERY hardly) to add missing parameters into > ffbonded.itp file f

[gmx-users] Re: Re: help with chromophore of a GFP

2013-03-25 Thread Anna MARABOTTI
Dear gmx-users, I'm still dealing with my problem of obtaining parameters for my chromophore of the GFP family, in order to treat it as a new residue. I'm trying (VERY hardly) to add missing parameters into ffbonded.itp file for AMBER99SB ff, using those parameters found in files calculated by

Re: [gmx-users] Re: Re: help with chromophore of a GFP

2013-03-22 Thread Mark Abraham
On Fri, Mar 22, 2013 at 2:36 PM, Anna MARABOTTI wrote: > > Dear Mark, Justin and other gmx-users, > thank you very much for your > help. Thanks to your suggestions, I made some steps forward, but still I > don't see the end of my travel... > > First of all, I would like to say > that my previou

[gmx-users] Re: Re: help with chromophore of a GFP

2013-03-22 Thread Anna MARABOTTI
Dear Mark, Justin and other gmx-users, thank you very much for your help. Thanks to your suggestions, I made some steps forward, but still I don't see the end of my travel... First of all, I would like to say that my previous problem was solved when I renamed O1 to OA. Justin was right. When I