Re: [gmx-users] Cytochrom C

HEME is in the charmm27 force field. bob h. On 1/5/2012 12:00 PM, Dariush Mohammadyani wrote: Yes, I have PDB file (1HRC.pdb). However, when I try to use "pdb2gmx" I get this error: Residue 'HEM' not found in residue topology database and HEM is Iron ion inside this protein. I do not know

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

mers For something like what I'm trying to do, where I"m using a pdb file that does not represent a protein, is On 1/4/2012 2:02 AM, Mark Abraham wrote: On 4/01/2012 4:57 PM, Robert Hamers wrote: I'd appreciate any help -- I'm trying to model a small (~ 20-carbon ) molec

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

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