Re: [gmx-users] popc

e the existing topologies with another gromos force field instead of reformatting all the ffG43a2x* files? What about the "atomtype 'CA' not found!" error? On Fri, Mar 21, 2008 at 12:57 PM, Justin A. Lemkul <[EMAIL PROTECTED]> wrote: > Quoting Chiara Parravicini <[EMAIL

[gmx-users] popc

Dear gromacs users, I would like to perform simulations of a protein embedded in popc, using a force field of the gromos series and I downloaded popc.pdb, popc.itp, lipid.itpa and the force field ffG43a2x extended for lipids. Looking throughout the archive I found different suggestions, but none

Re: [gmx-users] Noe distance restraints

ers the same is done. Thank you very much for your patience and your advices. Chiara On Fri, Feb 29, 2008 at 2:04 PM, Mark Abraham <[EMAIL PROTECTED]> wrote: > Chiara Parravicini wrote: > > > > Do you refer to pages 58-61 or 148-149 of the manual, about distance > > rest

Re: [gmx-users] Noe distance restraints

Do you refer to pages 58-61 or 148-149 of the manual, about distance restraints and NMR refinement? In that case is still not clear to me if the authors in the cited paper use simple distance restraints or apply NMR-derived data, given that the model presented is based on a X-Ray structure. So,

[gmx-users] Noe distance restraints

Dear Gromacs users, I'd like to perform a simulation following the protocol applied in the Ivanov's paper (*Molecular dynamics simulation of the P2Y14 receptor. Ligand docking and identification of a putative binding site of the distal hexose moiety.* *Bioorg. Med Chem Lett.* 2007;17(3):761-6. ).

Re: [gmx-users] Lennard Jones spheres

s using a structure with the ligand already inserted so, inspired by that papers, I was thinking about LJ spheres. How can I apply this approach with gromacs? Chiara On Feb 19, 2008 2:06 PM, Mark Abraham <[EMAIL PROTECTED]> wrote: > Chiara Parravicini wrote: > > Hi Mark, > >

Re: [gmx-users] Lennard Jones spheres

Hi Mark, I just want make use of the volumes of the spheres to enlarge the pocket without the use of any ligands. Thanks in advance! Chiara On Feb 19, 2008 1:12 AM, Mark Abraham <[EMAIL PROTECTED]> wrote: > Chiara Parravicini wrote: > > Hi gromacs users, > > > > I w

[gmx-users] Lennard Jones spheres

Hi gromacs users, I would like to add LJ spheres into the protein cavitities, but I don't know how to define input parameters and files to set the run. Should I define spheres as "dummy atoms"? Any suggestion will be greatly appreciated! Thanks in advance, Chiara

[gmx-users] NOE distance restraints

Dear Gromacs users, I intend to perform a MD simulation of a GPCR model applying distant restraints to the backbone of alpha helices, something like NOE distance restraints. I guess that gromacs can't do it directly but if I've well understand I can manually provide classical distance restraints i