| 5:08:47 PM PDT - Fri, May 4th 2012 |
|
I have similar question
|
Is there anyone who knows the answer? I have similar or the same question with what Lemonseed asked.
Now I'm trying to find the way to keep bonds between atoms within a molecule while doing optimization task.
Now I'm doing QM/MM simulation and trying to optimize a system which contains amino acids in water.
I guess, since amino acids are in aqueous state, some part of them like "COOH" or "NH2" loss or get "H"
By this, the amino acids becomes partially charged and in some cases the whole amino acids becomes ion state.
(Am I right?)
I have pdb files of amino acids that is in partially charged state or ion state.
I placed this pdb file in solvation box by doing prepare task, and runned optimization task.
When the task is over, I checked the output xyz file and found that partially charged region became neutral!
Furthermore, in some cases a hydrogen atom was attached to a part of amino acid where it shouldn't be.
(for example, a hydrogen atom was attached to a carbon atom in benzene ring in amino acid so thatthat carbon atom has 2 hydrogen bond and 2 carbon bond)
I have another question about this. When I run optimization task, the amino aicds moves from their initial position. I don't want to exclude the amino acids in my calculation but just want to fix them in their initial position.
Is there any method to fix certain molecule or atom in their initial position while doing optimization task or other simulation?
If you knows the answer or some hints about the questions, please teach me.
|