[gmx-users] grouping custom ions
nedomacho at gmail.com
Thu Jul 26 00:08:55 CEST 2018
Ah. Upon actually checking my oplsaa.ff directory, i don't have this file.
Could this info be somewhere else?
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?
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
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