[gmx-users] about toplogy file

Hello all, I am trying to understand the topology file for gromacs. so as to make n-alkane chain. for that I have dihedral parameters of periodic type. In the manual it says that With the periodic GROMOS (dihedral ) potential a special 1-4 LJ-interaction must be included; for this reason I set ge

Re: [gmx-users] query about making a pdb file

Another handy bit of software for model building is Ecce http://ecce.emsl.pnl.gov/ At 02:07 PM 3/29/2007, you wrote: PyMOL (http://pymol.sf.net) is one option for building the chain based on natural amino acids and subsequently performing mutations. Jay On Wed, 28 Mar 2007, Jagannath Mondal

Re: [gmx-users] Missing LJ interaction

Steve Fiedler wrote: Thank you for looking over the input and for suggestions Mark. Unfortunately, a comparison of the topologies with diff revealed no inconsistencies. GROMACS can correctly recognize the presence of the significant repulsion (e+10) between atoms 1 and 5 when the atoms from

Re: [gmx-users] Missing LJ interaction

Thank you for looking over the input and for suggestions Mark. Unfortunately, a comparison of the topologies with diff revealed no inconsistencies. GROMACS can correctly recognize the presence of the significant repulsion (e+10) between atoms 1 and 5 when the atoms from both triatomic molecul

Re: [gmx-users] Re: bug in ffoplsaanb.itp?

Alan, Thanks. That's very helpful. I'm actually not using OPLS at all myself -- I just stumbled across this really odd looking set of F- parameters when troubleshooting for someone else. Anyway, your comments are very helpful. I appreciate it. David On 3/31/07, Alan Chen <[EMAIL PROTECTED]> wro