[gmx-users] No default bond types

[Justin Lemkul]

On 3/25/20 7:59 PM, Neena Susan Eappen wrote:
> Hi Justin,
>
> Yes errors from grompp are very clear. Initially, I had errors for all four 4 new bond and 9 new angle types, grompp specifically stated which line in the topology file was missing. Accordingly, I added parameters for all in the ffbonded.itp file correctly. Even after that, I still wonder why I have errors....

You haven't provided any information from which we can diagnose the 
issue, but if you're still having errors related to missing parameters, 
you have still not correctly added the required parameters.

If you need further help, you'll have to provide the exact error 
messages and any other relevant information about what you're doing, 
topology snippets, etc.

-Justin

>
> ________________________________
> From: Neena Susan Eappen <neena.susaneappen at mail.utoronto.ca>
> Sent: Wednesday, March 25, 2020 8:23 PM
> To: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: Re: [gmx-users] No default bond types
>
> Hi Alessandra,
>
> For the 4 new bond types and 9 new angle types, I modified the ffbonded.itp file. However, the command grompp gave error for one bond and 6 angle types although I have all in there. Is there a way to resolve this?
> ________________________________
> From: Neena Susan Eappen
> Sent: Wednesday, March 25, 2020 3:17 AM
> To: gromacs.org_gmx-users at maillist.sys.kth.se <gromacs.org_gmx-users at maillist.sys.kth.se>
> Subject: [gmx-users] No default bond types
>
> Hello gromacs users,
>
> I just modified opls force field for a modified aminoacid with 4 new bond types and 9 new angle types. However, the command grompp gave a no default error for one bond and 6 angle types. Is there a way to resolve this?
>
> Many thanks and Take care,
> Neena
>

-- 
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Justin A. Lemkul, Ph.D.
Assistant Professor
Office: 301 Fralin Hall
Lab: 303 Engel Hall

Virginia Tech Department of Biochemistry
340 West Campus Dr.
Blacksburg, VA 24061

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

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