[gmx-users] Computational Alanine Scanning

Lucio Ricardo Montero Valenzuela lucioric at ibt.unam.mx
Tue May 18 18:41:36 CEST 2010

When you re-generate hydrogens, you are introducing some extra disorder
to the system. What I did is to write a script to rename the hydrogens.
For example, there are residues that have the hydrogen numbering
starting from 2 (eg. hydrogens on CB of lysine had hydrogens starting
from HB2). In the script I renamed the hydrogens to start on number 1.
Also I had to rename ILE atoms (C|H)D1? to (C|H)D?, where (C|H) stands
for carbon or hydrogen and ? stands for any character. Also I had to
rename atoms in the N and C terminus. When you have doubt in the atom
naming, you can see in the RTP file. After doing that, so I didn't have
to re-generate hydrogen, I got a smooth energy graph in the EM, that I
didn't get by re-generating the hydrogens. Re-generating hydrogens and
also re-generating atomic velocities introduce disorder to your system.
Best regards.

Lucio Montero.
Laboratorio del Dr. Federico Sánchez
Ext. 27666
Departamento de Biología Molecular de Plantas
Instituto de Biotecnología, UNAM
Cuernavaca, Morelos, 62210

El mar, 18-05-2010 a las 14:22 +1000, Mark Abraham escribió:
> ----- Original Message -----
> From: Binh Khanh Mai <khanhbinh183 at yahoo.com>
> Date: Tuesday, May 18, 2010 14:10
> Subject: [gmx-users] Computational Alanine Scanning
> To: gmx-users at gromacs.org
> -----------------------------------------------------------
> | 
> > 
> > 
> > Dear all,
> >     I'm trying use GROMACS to calculate binding free energy with MM-PBSA method and do Computational Alanine Scanning. After run MD and obtain pdb files, I use PYMOL to mutate one residue to Alanine to estimate the energy difference between 2 structures. My issue is that I don't know how to generate topology file (.top file) after mutation but not ignore hydrogen in initial file. If using pdb2gmx command, it needs me ignore hydrogen and I think hydrogen after using this command is not in the same place with hydrogen at first. This will my my results unbelievable.
> Do your mutation with PYMOL, and later plan to use those coordinates as inputs to grompp. Use pdb2gmx however you need to in order to create the new .top. Assuming PYMOL is not messing around with atom/residue naming and ordering except for the mutated residue, all you have to do is edit a copy of the PYMOL coordinate file so that the new residue has atom names, residue names and atom ordering that match the .top. Then supply the .top with the fixed coordinate file to grompp.
> Alternatively, work out why pdb2gmx requires you to ignore and regenerate hydrogens, and fix the issue there.
> Mark

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