[gmx-users] HID error in amber14sb.ff

[Hongbin Wan]

Sorry about the continuous email.  I think I solved this issue.

For HID and HIP, they used different atom types for CD2.
CV for HID and CW for HIP.

Thanks for helping.

--Hongbin

On Wed, Aug 17, 2016 at 10:53 AM, Hongbin Wan <tuf74538 at temple.edu> wrote:

> 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
>> > > --
>> > > Gromacs Users mailing list
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>
>
>
> --
> Hongbin Wan
>
> *Department of Chemistry*
>
> *130 Beury Hall*
>
> *1901 N 13th Street*
>
> *Philadelphia, PA 19122*
>
> Email: tuf74538 at temple.edu
>



-- 
Hongbin Wan

*Department of Chemistry*

*130 Beury Hall*

*1901 N 13th Street*

*Philadelphia, PA 19122*

Email: tuf74538 at temple.edu