[gmx-users] No default bond types

[Justin Lemkul]

On 3/25/20 8:47 PM, Neena Susan Eappen wrote:
> I am sorry that I previously did not attach any files as I was confident how I edited. Problem Solved: By just adding those missing parameters in the topology file itself. I am showing values below for future reference:
>
> On grompp, following error came up:
>
> ERROR 1 [file topol.top, line 84]:
>    No default bond types
>
>   Line 84 in topol.top :  14    20     1
>
> Which corresponds to a bond between CA and C15 (atoms 14 and 20) in a modified alanine residue, for which I already had parameters in the ffbonded.itp file under [ bond types] as shown below:
>
> CA    C15     1    0.14900   334720.0

This didn't work because ffbonded.itp requires atom types, not atom names.

-Justin

> Problem solved by changing that line 84 in topology file
>
>    Line 84: 14    20     1        0.14900   334720.0
>
> ________________________________
> From: Neena Susan Eappen <neena.susaneappen at mail.utoronto.ca>
> Sent: Wednesday, March 25, 2020 11:59 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 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....
>
>
> ________________________________
> 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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