[gmx-users] change atom type in ffbonded.itp

Justin Lemkul jalemkul at vt.edu
Sat Nov 5 15:49:03 CET 2016

On 11/5/16 10:31 AM, ‪sky sky‬ ‪ wrote:
> Hi justin.
> Excuse me ask you againI attached my residue topology file in this e-mail.I geting this information from cgenff server and include in the force field (charmm27).I have this error:

Most of the parameters you need are already available in our CHARMM36 port, 
which includes CGenFF.  There are parameters you will have to add, but most of 
what you need is already there, which will simplify your life a lot.

> ERROR 1 [file ffbonded.itp, line 259]:  Not enough parameters
> CGENFF does not geve me information related to ub0 and cub so, I changed ub0 and cub parts in ffbonded.itp.so no errors.ubo= 0.00cub= 0.00Now.I can change this infomations?If no,so how can i geting information related ubo and cub in ffbonde.itp?How to can generate this numbers?What is cth ,ub0 and cub ??
> tanks a lot.

These are Urey-Bradley parameters.  ub0 is the equilibrium 1-3 distance and cth 
is the harmonic force constant associated with the 1-3 stretch.


>       From: Mostafa Khedrinia <mostafakhedrinia at gmail.com>
>  To: gromacs.org_gmx-users at maillist.sys.kth.se
>  Sent: Tuesday, 1 November 2016, 15:10:32
>  Subject: [gmx-users] change atom type in ffbonded.itp
> hello
> I'm using Gromacs with
> charm27.ff force-field.I adding a new residue (NAG) in force field
> I have a problem with water molecules in my system: During
> minimization, I have this message:
> step X: Water molecule starting at atom XXX can not be settled.
> Check for bad contacts and/or reduce the timestep if appropriate.
> Wrote pdb files with previous and current coordinates
> My problem is related to protein structure.I changed angletypes part in
>  ffbonded.itp .  so not errors.
> my question:
> This change how much is true?


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


More information about the gromacs.org_gmx-users mailing list