[gmx-users] Amber and protonation state

Arik Cohen acohen at biochem.duke.edu
Fri Feb 26 20:38:03 CET 2010

Thanks a lot for the quick response


On 2/26/2010 3:54 AM, Justin A. Lemkul wrote:
> Arik Cohen wrote:
>> Dear users,
>> I would be most thankful for any comment or advice on the following 
>> problems:
>> 1. I'm running GROMACS 4.04 with amber V_4.0. /amber99sb forcefield. 
>> While executing the pdb2gmx command as: pdb2gmx -f 1bgq.pdb -water 
>> tip3p -his
>> the -his option does not work regardless of the choice in the 
>> protonation state
>> 2. Is there any way to change the protonation state not via an 
>> interacticve mode and thus to enable to run the pdb2gmx in an 
>> automatic way(echo 10 | pdb2gmx ... | -his echo 2 will not work of 
>> course)
> Point #10 in the ffamber "Installation and Testing" section:
> http://chemistry.csulb.edu/ffamber/#install
> You can solve all protonation issues by having the right residue names 
> to start.  The Gromacs conventions for, e.g. histidine, are HISA, 
> HISB, and HISH.  For Amber, the corresponding residue names are HID, 
> HIE, and HIP.  If you go through your .pdb file and re-name residues 
> in advance, the proper protonation states will be assigned.  This also 
> applies to any other titratable residues, and termini, which must be 
> prefixed with N and C.
> -Justin
>> Thanks a lot
>> Arik

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