On 8/27/14, 6:25 AM, RINU KHATTRI wrote:
hello justin but what is the use of this command -missing for at least
one missing residues shall we use this or not
For a missing residue within the chain, you should absolutely not use -missing.
If you do, you will have a flawed model that will al
hello justin but what is the use of this command -missing for at least
one missing residues shall we use this or not
On Mon, Aug 25, 2014 at 6:38 PM, Justin Lemkul wrote:
>
>
> On 8/25/14, 1:31 AM, RINU KHATTRI wrote:
>>
>> use -missing in last of command pdb2gmx
>>
>
> This is extremely dangerou
On 8/25/14, 1:31 AM, RINU KHATTRI wrote:
use -missing in last of command pdb2gmx
This is extremely dangerous and in should not be done in the case of missing
residues as it will lead to a broken and useless topology.
-Justin
On Mon, Aug 25, 2014 at 10:54 AM, neha bharti wrote:
Hello A
Dear Neha,
It is right as per my opinion. if the end residue is missing no issue.
join the ligand pdb and receptor pdb and use pdb2gmx directly .
no need to do as per total process of Justin tutorial. As justin tutorial
is
for the non-amino acid residues.
use properly the pdb2gmx command a
Hello Rama david
Thank you very much for your reply.
The residue is missing from the middle as well as from the end. Hence I
have modeled it with the help of homology modeling.
Then I align both the protein (PDB downloaded as well as homology modelled)
and get a RMSD fluctuation of 0.45 with the
Hello Rama david
Thank you very much for your reply.
The residue is missing from the middle as well as from the end. Hence I
have modeled it with the help of homology modeling.
Then I align both the protein (PDB downloaded as well as homology modelled)
and get a RMSD fluctuation of 0.45 with the
Dear Neha,
the question depend on which residue is missing??
Is the residue is from middle or from end that is important.
If end residue is missing then no issue. but middle residue is problematic.
you can model the protein and then align it with pymol align command or any
other visualizing
use -missing in last of command pdb2gmx
On Mon, Aug 25, 2014 at 10:54 AM, neha bharti wrote:
> Hello All
>
> I am performing Molecular dynamics simulation of protein-ligand complex
> using charmm36 force field in popc lipid.
>
> I downloaded the protein ligand complex pdb file. And as mentioned i
Hello All
I am performing Molecular dynamics simulation of protein-ligand complex
using charmm36 force field in popc lipid.
I downloaded the protein ligand complex pdb file. And as mentioned in
Justin A. Lemkul protein-ligand complex tutorial I have seperate ligand and
protein from pdb file.
My
