[gmx-users] Adding a residue

2009-08-13 Thread Smith, Chanel Chonda
Hello, I am currently using GROMACS 4. When trying to process the pdb file with pdb2gmx, an error message came up stating that a particular residue was not recognized by the residue topology database. I then tried to adding a molecule in the ffrtp file and adding the name in aminoacids.da

RE: [gmx-users] Adding a residue

2009-08-14 Thread Smith, Chanel Chonda
, Chanel Chonda wrote: > Hello, > I am currently using GROMACS 4. When trying to process the pdb file > with pdb2gmx, an error message came up stating that a particular residue was > not recognized by the residue topology database. I then tried to adding a > molecule in the ff.

[gmx-users] PRODRG

2009-10-07 Thread Smith, Chanel Chonda
Hello, I have recently made a pdb file using the Dundee PRODRG server. However, when I try to use this pdb in gromacs, I receive an error message that states: "DRG is not in the topology database." I have tried to use the available tutorial to solve this issue, but with not much success. Cou

RE: [gmx-users] PRODRG

2009-10-07 Thread Smith, Chanel Chonda
In the drug-enzyme tutorial it says that the crude was refined using a certain force field, SD, and CG. How was this accomplished? -Original Message- From: gmx-users-boun...@gromacs.org on behalf of Justin A. Lemkul Sent: Wed 10/7/2009 1:11 PM To: Discussion list for GROMACS users Subject:

[gmx-users] Force Fields

2009-11-19 Thread Smith, Chanel Chonda
What are the main differences between the force fields used in gromacs? In which scenarios are each force field better to use? Chanel -- gmx-users mailing listgmx-users@gromacs.org http://lists.gromacs.org/mailman/listinfo/gmx-users Please search the archive at http://www.gromacs.org/search