[gmx-users] grouping custom ions

[Justin Lemkul]

On 7/25/18 5:12 PM, Alex wrote:
> Ah. Upon actually checking my oplsaa.ff directory, i don't have this file.
> Could this info be somewhere else?

It's in $GMXLIB. It's not a per-force field thing.

> Another question, while we're at it: the file 'atomtypes.atp' is basically
> a table with atomic masses. Over a few years, I have added a bunch of new
> atomtypes without modifying this file. Would that be a problem?

This file is only used by pdb2gmx, so depending on how you're generating 
topologies, it may not matter.

-Justin

> Thanks,
>
> Alex
>
> On Wed, Jul 25, 2018 at 2:36 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>
>>
>> On 7/25/18 4:35 PM, Alex wrote:
>>
>>> Hi all,
>>>
>>> Perhaps a trivial question here. I added a few custom metal ions into
>>> oplsaa's 'ions.itp' and 'ffnonbonded.itp' -- everything works fine. There
>>> is, however, a problem with selecting them in e.g. trjconv without using a
>>> custom index. Example: 5 NA, 6 CL, and 1 XX (custom) ions in the system.
>>> The group "Ion" now only contains 11 elements (NA + CL), while I'd like to
>>> select all 12 with "Ion". Things are scripted, so it would be really nice
>>> to be able to do that without additional indexing.
>>>
>>>
>> Update residuetypes.dat to include your new ions.
>>
>> -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

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