[gmx-users] Writing PDB file so that protonation state of HIS is explicit by name

[Dawid das]

So they were. How should I modify my trjconv command to get this effect?
Because with

gmx trjconv -f npt-md-prod-center.xtc -o npt-md-prod-3ns.pdb -pbc mol
-center -s npt-md-prod.tpr -ndec 6 -tu ns -b 3 -e 3

I don't and I don't really see this option when calling gmx trjconv -h.

2018-04-23 17:18 GMT+02:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 4/23/18 11:15 AM, Dawid das wrote:
>
>> Dear All,
>>
>> Is it possible to create PDB file from XTC so that naming of histidine
>> residues
>> is HSE, HSD, HSP instead of HIS?
>>
>
> Yes, but only if they were named as such in the topology and therefore in
> the .tpr file being used to do the conversion.
>
> -Justin
>
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