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

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

Can you please give me an example of such a modeling software?
I tried it with PYMOL but the results are not very good.
And I also found several programs but the are all not free.

Thank you,
Eva

>
>
> On 7/12/12 6:12 AM, reisingere at rostlab.informatik.tu-muenchen.de wrote:
>> 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?
>>
>
> Yes.  The capping groups (see your force field's .rtp file for available
> entries) are treated as any other residue.  Gromacs will not magically
> build
> them; they need to be present.
>
>> But how can I add the capping groups to the structure?
>>>
>
> You'll have to use some external modeling software for that.
>
> -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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