[gmx-users] No default bond types

[Neena Susan Eappen]

Interesting, I did have that line in ffnonbonded.itp

opls_968   C15  6      12.01100     0.641       A    3.55000e-01  3.17984e-01
________________________________
From: Neena Susan Eappen <neena.susaneappen at mail.utoronto.ca>
Sent: Thursday, March 26, 2020 1:04 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

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
________________________________
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