Re: [gmx-users] termini modification

2011-08-27 Thread Justin A. Lemkul
lina wrote: pdb2gmx -ter I doubt this is of any use; the Amber force fields don't use the same conventional termini selection that the other force fields do, as the OP states. I suspect that's why the .tdb approach is not working. I think the best approach is to simply write .rtp entrie

Re: [gmx-users] termini modification

2011-08-27 Thread lina
pdb2gmx -ter On Sat, Aug 27, 2011 at 6:17 PM, Vijayaraj wrote: > Hello, > > I am using gromacs 4.5.4 with amber99sb ff. I would like to modify the > terminal residues from NALA and CALA to normal ALA (just as middle > residues). As the terminal selection option is not enabled with the amber > ff,

[gmx-users] termini modification

2011-08-27 Thread Vijayaraj
Hello, I am using gromacs 4.5.4 with amber99sb ff. I would like to modify the terminal residues from NALA and CALA to normal ALA (just as middle residues). As the terminal selection option is not enabled with the amber ff, I am using the termini modification parameters with aminoacids.c.tdb. here