[gmx-users] HID error in amber14sb.ff

[Hongbin Wan]

Hi,

Thanks a lot for helping.

You are right about the atom types of each atom within this error, which
are CB-CG-CD2-ND1.

And I followed your logic to add one line to file ffbonded.itp.

Do I need to do anything else to let gromacs load the file?  because adding
this line won't solve the error.

My thoughts:

I think pd2gmx will load forcefield.itp where has the option to load
ffbonded.itp.

--Hongbin


this is the line with error "No default Improper Dih. types"

 373   376   382   377     4

The following lines are from .gro file.

   23HID      N  369   0.914   4.779   2.151

   23HID      H  370   0.842   4.748   2.089

   23HID     CA  371   0.882   4.835   2.283

   23HID     HA  372   0.947   4.910   2.294

   23HID     CB  373   0.749   4.894   2.286

   23HID    HB1  374   0.747   4.967   2.217

   23HID    HB2  375   0.735   4.934   2.376

   23HID     CG  376   0.638   4.808   2.260

   23HID    ND1  377   0.543   4.833   2.167

   23HID    HD1  378   0.545   4.907   2.100

   23HID    CE1  379   0.445   4.744   2.178

   23HID    HE1  380   0.366   4.738   2.116

   23HID    NE2  381   0.463   4.665   2.281

   23HID    CD2  382   0.592   4.699   2.330

   23HID    HD2  383   0.641   4.651   2.404

On Wed, Aug 17, 2016 at 3:34 AM, Nicolas Cheron <
nicolas.cheron.boulot at gmail.com> wrote:

> Hi,
>
> I had this problem and wrote to Viet Man who uploaded the force field. I am
> quoting his answer:
>
> I have found the error come from HIP residues, diheral angle CB-CG-CD2-ND1
> (=
> CT-CC-CW-NA). It causes by missing the improper dihedral angle information.
> To solve it, you may open file ffbonded.itp and add below line under line
> 730th
> NA  CW  CC  CT       4      180.00     4.60240     2
>
> Nicolas
>
>
>
> 2016-08-16 20:28 GMT+02:00 Mark Abraham <mark.j.abraham at gmail.com>:
>
> > Hi,
> >
> > Please search the archives - you're not the first person to notice that
> > with the user-contributed port of amber14, but nobody's reported back
> where
> > the problem might be.
> >
> > Mark
> >
> > On Tue, Aug 16, 2016 at 7:48 PM Hongbin Wan <tuf74538 at temple.edu> wrote:
> >
> > > Hi all,
> > >
> > > I am trying to run MD simulations with *amber14sb.ff (downloaded from
> > > gromacs forcefiled web)*
> > >
> > > However, it always shows * No default Improper Dih. types *for HID when
> > to
> > > use grompp. Could anyone tell me how to solve this issue?
> > >
> > > I had tried other forcefields, and they worked well.
> > >
> > > Thanks!!
> > > -Hongbin
> > > --
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-- 
Hongbin Wan

*Department of Chemistry*

*130 Beury Hall*

*1901 N 13th Street*

*Philadelphia, PA 19122*

Email: tuf74538 at temple.edu