Re: [gmx-users] Missing Residues of PDB file

2014-08-27 Thread RINU KHATTRI
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 jalem...@vt.edu wrote: On 8/25/14, 1:31 AM, RINU KHATTRI wrote: use -missing in last of command pdb2gmx This is extremely

Re: [gmx-users] Missing Residues of PDB file

2014-08-27 Thread Justin Lemkul
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

Re: [gmx-users] Missing Residues of PDB file

2014-08-25 Thread rama david
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

Re: [gmx-users] Missing Residues of PDB file

2014-08-25 Thread neha bharti
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

Re: [gmx-users] Missing Residues of PDB file

2014-08-25 Thread rama david
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

Re: [gmx-users] Missing Residues of PDB file

2014-08-25 Thread Justin Lemkul
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

[gmx-users] Missing Residues of PDB file

2014-08-24 Thread neha bharti
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

Re: [gmx-users] Missing Residues of PDB file

2014-08-24 Thread RINU KHATTRI
use -missing in last of command pdb2gmx On Mon, Aug 25, 2014 at 10:54 AM, neha bharti nehabharty...@gmail.com 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.

[gmx-users] missing residues in PDB file

2014-03-19 Thread Guo, Yanan
Hello dear gmx-users, I want to transform a .pdb file to a .gro file using pdb2gmx. But there are some missing residues in my .pdb file. How should I add these missing residues to the .pdb file? Any suggestion is appreciated. Thank you very much! Cheers Yanan -- Gromacs Users mailing list *

Re: [gmx-users] missing residues in PDB file

2014-03-19 Thread Andres Ortega Guerrero
You could add them with modeller or rosseta, Andrés Ortega Ing. Electrónica Universidad del Valle El 19/03/2014, a las 14:36, Guo, Yanan yanan@partner.kit.edu escribió: Hello dear gmx-users, I want to transform a .pdb file to a .gro file using pdb2gmx. But there are some missing

Re: [gmx-users] missing residues in pdb file

2013-12-14 Thread Justin Lemkul
On Sat, Dec 14, 2013 at 7:03 AM, delara aghaie d_agh...@yahoo.com wrote: Dear Gromacs users, I am going to simulate human serum albumin( HSA) .. The pdb file contains warfarin as well. Now I have two questions: 1) to delete warfarin which lines should be removed? only those starting with