[gmx-users] more than one protonation per residue with pdb2gmx

[reisingere at rostlab.informatik.tu-muenchen.de]

Hi Justin,
so you mean that I first have to add the capping groups to my structure
and then run pdb2gmx with the -ter function?

But how can I add the capping groups to the structure?
>
>
> On 7/12/12 4:37 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>> I have another question about the option -ter of the pdb2gmx command.
>>
>> I choose it because I thought that this is a way that I can determine
>> what
>> shell happen with the termini but I was not ask anything by the program.
>>
>> My aim is it to block the termini with a neutral group. Is there a way
>> to
>> do this with gromacs?
>>
>
> Yes.  You need to build the appropriate groups onto your protein's
> structure
> using normal capping groups present within the force field (ACE, NME, NH2,
> etc)
> and choose "None" for the termini when running pdb2gmx so that no
> additional
> protons are added or removed; the first and last amino acids are then
> treated as
> internal residues with normal peptide bonds.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul, Ph.D.
> Research Scientist
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
> ========================================
>
>
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