[gmx-users] No default bond types

[Justin Lemkul]

On 3/25/20 9:04 PM, Neena Susan Eappen wrote:
> Thank you Justin, but I had already defined it as C15 in atomtypes.atp for ALH (modified alanine)
>
>   opls_968   12.01100  ; C15 in ALH

atomtypes.atp is irrelevant after pdb2gmx, so grompp has no knowledge of 
it. You need to add it to ffnonbonded.itp and include the bonded atom 
type (C15 in this case) as the second column so that grompp understands 
the translated atom type.

-Justin

> ________________________________
> From: Neena Susan Eappen <neena.susaneappen at mail.utoronto.ca>
> Sent: Thursday, March 26, 2020 12:47 AM
> 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
>
> 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
>
> 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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