Re: [gmx-users] Help with non-standard residues and molecular structures

2012-01-04 Thread Mark Abraham
On 4/01/2012 4:57 PM, Robert Hamers wrote: I'd appreciate any help -- I'm trying to model a small (~ 20-carbon ) molecule linked to a diamond surface. I got the diamond surface with 1500 atoms working fine all the way through to the MD simulation and it looks great. But I'm getting stuck

Re: [gmx-users] Help with non-standard residues and molecular structures

2012-01-04 Thread Robert Hamers
Thanks-- that clarifies a lot. I hadn't quite realized how much is assumed about the residue terminii. It seems like I was trying to fit a square peg into a round hole. I'm going to re-think this and maybe take a different approach just based on using HETATMs and not trying to define a

[gmx-users] Help with non-standard residues and molecular structures

2012-01-03 Thread Robert Hamers
I'd appreciate any help -- I'm trying to model a small (~ 20-carbon ) molecule linked to a diamond surface. I got the diamond surface with 1500 atoms working fine all the way through to the MD simulation and it looks great. But I'm getting stuck on the molecule, which is not a protein but