[gmx-users] on PDB2gmx

Acoot Brett acootbrett at yahoo.com
Sun Apr 8 08:50:42 CEST 2012

Hi Peter,
I mean if before we input the pdb file to the pdb2gmx, we predetermine the protonation state of HIS, then the corrected PDB file will decide the protonation state of HIS, rather pdb2gmx will assign the protonation state, as for the coordinates of the protonation H will exist in the corrected PDB file.
I guess according to your one previous e-mail that we can still keep the code for different protonation HIS as HIS, and with -his in the pdb2gmx, pdb2gmx will not make wrong. But it seems the -his function would be useless (maybe I am not right on it).
The other possibility is that we will change diffrent protonation state HIS with different HIS codes according to the GROMACS manual. But in this situation we will use .rtp file. Can you tell me how to get and use the .rtp file?

----- Original Message -----
From: Peter C. Lai <pcl at uab.edu>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Saturday, 7 April 2012 11:58 AM
Subject: Re: [gmx-users] on PDB2gmx

On 2012-04-06 06:41:57PM -0700, Acoot Brett wrote:
> Dear All,
> Can I remove all the H from the PDB file and then input it to the pdb2gmx so that pdb2gmx can produce all the correct protonation state of the protein residues including HIS?
> Cheers,
> Acoot   

It will not do what you expect. There is no "magical way" for pdb2gmx to  
determine HIS protonation. The best it can do is calculate potential H-bonding
and assign protons from there; and there is no guarantee it will be "correct"
or fit your expectations. You should really determine what criteria to choose
for histidine protonation state and assign them manually for best effect.

Justin already answered this question in a different way. Perhaps there is a
language barrier/problem involved?

Peter C. Lai            | University of Alabama-Birmingham
Programmer/Analyst        | KAUL 752A
Genetics, Div. of Research    | 705 South 20th Street
pcl at uab.edu            | Birmingham AL 35294-4461
(205) 690-0808            |

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