[gmx-users] grouping custom ions
jalemkul at vt.edu
Thu Jul 26 01:41:08 CEST 2018
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.
> 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 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
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Justin A. Lemkul, Ph.D.
Virginia Tech Department of Biochemistry
303 Engel Hall
340 West Campus Dr.
Blacksburg, VA 24061
jalemkul at vt.edu | (540) 231-3129
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