subject:"\[gmx\-users\] Cyclic Peptide Topology"

Re: [gmx-users] Cyclic Peptide Topology

2013-07-14 Thread Justin Lemkul

On 7/14/13 7:07 PM, jriedel wrote: Hi, I'm want to run a MD simulation with a Phe-Phe-Phe-Phe-Gly cyclic peptide. But I'm have problems generating the topology files. When I try to use the strategy to generate a topology file for the linear GF using pdb2gmx -ff charmm27 -f pep.pdb -o pep.g

[gmx-users] Cyclic Peptide Topology

2013-07-14 Thread jriedel

Hi, I'm want to run a MD simulation with a Phe-Phe-Phe-Phe-Gly cyclic peptide. But I'm have problems generating the topology files. When I try to use the strategy to generate a topology file for the linear GF using pdb2gmx -ff charmm27 -f pep.pdb -o pep.gro -ter -water spce and choosing None f