On Sat, Oct 18, 2014 at 9:59 PM, Agnivo Gosai
wrote:
> Dear Users
>
> Thrombin-Aptamer complex : PDB ID 1HAO
>
> Thanks for the earlier comments. I appreciate the efforts of all users and
> developers for taking their time out and helping.
>
> I checked the pdb file for the "occupancies" not equa
On 10/18/14 3:59 PM, Agnivo Gosai wrote:
Dear Users
Thrombin-Aptamer complex : PDB ID 1HAO
Thanks for the earlier comments. I appreciate the efforts of all users and
developers for taking their time out and helping.
I checked the pdb file for the "occupancies" not equal to 1.000 and found 9
Dear Users
Thrombin-Aptamer complex : PDB ID 1HAO
Thanks for the earlier comments. I appreciate the efforts of all users and
developers for taking their time out and helping.
I checked the pdb file for the "occupancies" not equal to 1.000 and found 9
atoms having 0.001 ocuupancy. So, I manually
On 10/17/14 6:08 PM, Agnivo Gosai wrote:
Dear Gromacs Users
I am working with a complex of Human Thrombin - DNA aptamer ( pdb id 1HAO )
. I am using GROMACS 4.5.7 having the force field AMBER99SB-ParmBSC0 ported
into it. I had cleaned the PDB file off crystal waters and a small chemical
ligand
Does the pdb file have alternative conformations for some side chains or
atoms?
Like a side chain may have 50% chance to be rotated left, and 50% chance to
be rotated right.
The crystallographer recognized these two possibilities, and give each
possibility a 0.5 occupancy.
It may look like
LYSA
Dear Gromacs Users
I am working with a complex of Human Thrombin - DNA aptamer ( pdb id 1HAO )
. I am using GROMACS 4.5.7 having the force field AMBER99SB-ParmBSC0 ported
into it. I had cleaned the PDB file off crystal waters and a small chemical
ligand ( which I dont require ) before passing it t
