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

[Justin Lemkul]

On 4/23/18 11:23 AM, Dawid das wrote:
> 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.

The only source of residue names is the .tpr file. If trjconv is not 
giving you what you want, then the residues are not named as you claim. 
You can dump the contents of the .tpr with gmx dump or write a PDB 
straight from it with editconf to confirm what it has in it.

-Justin

> 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
>>
>> --
>> ==================================================
>>
>> Justin A. Lemkul, Ph.D.
>> Assistant Professor
>> Virginia Tech Department of Biochemistry
>>
>> 303 Engel Hall
>> 340 West Campus Dr.
>> Blacksburg, VA 24061
>>
>> jalemkul at vt.edu | (540) 231-3129
>> http://www.thelemkullab.com
>>
>> ==================================================
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-- 
==================================================

Justin A. Lemkul, Ph.D.
Assistant Professor
Virginia Tech Department of Biochemistry

303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061

jalemkul at vt.edu | (540) 231-3129
http://www.thelemkullab.com

==================================================