Re: [gmx-users] Charmm36 in Gromacs: missing dihedrals

2011-05-25 Thread Jon Fuller
Dear Mark and Justin, Thanks for the quick reply. I must have misunderstood the procedure. I was assuming that the generated top file should include the actual values used for the Urea-Bradley terms. Previously I have only included molecules using an itp file and was expecting similar behaviour.

Re: [gmx-users] Charmm36 in Gromacs: missing dihedrals

2011-05-25 Thread Justin A. Lemkul
Jon Fuller wrote: Dear all, I thought that I would reply to this thread as I am having similar problems and there didn't seem to be an obvious solution. I wanted to run a simulation of a POPE bilayer using the Charmm36 parameters from the Gromacs website. So I used pdb2gmx to generate a .top f

Re: [gmx-users] Charmm36 in Gromacs: missing dihedrals

2011-05-25 Thread Mark Abraham
On 25/05/11, Jon Fuller wrote: > Dear all, > > I thought that I would reply to this thread as I am having similar > problems and there didn't seem to be an obvious solution. > I wanted to run a simulation of a POPE bilayer using the Charmm36 > parameters from the Gromacs website. So I used pdb

Re: [gmx-users] Charmm36 in Gromacs: missing dihedrals

2011-05-25 Thread Jon Fuller
Dear all, I thought that I would reply to this thread as I am having similar problems and there didn't seem to be an obvious solution. I wanted to run a simulation of a POPE bilayer using the Charmm36 parameters from the Gromacs website. So I used pdb2gmx to generate a .top file. I used the input