[gmx-users] Full topology from pdf2gmx

[Eric Smoll]

Hello Justin,

Thank you for the response. It looks like grompp -pp only expands includes,
it does not add unspecified force constants to directives (bonds, angles,
etc.)

Best,
Eric

On Wed, Aug 3, 2016 at 4:13 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 8/3/16 11:18 AM, Eric Smoll wrote:
>
>> Hello GROMACS users,
>>
>> Pdb2gmx generates a topology without parameters under directives like
>> bonds, angles, etc. This is because it references information in the
>> specified forcefield database. Is it possible to generate a fully
>> populated
>> topology with force constants, equilibrium distances, etc.?
>>
>>
> Try grompp -pp.
>
> -Justin
>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalemkul at outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==================================================
> --
> Gromacs Users mailing list
>
> * Please search the archive at http://www.gromacs.org/Support
> /Mailing_Lists/GMX-Users_List before posting!
>
> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>
> * For (un)subscribe requests visit
> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> send a mail to gmx-users-request at gromacs.org.
>