[gmx-users] on HS14 atomtype

[Sarath Chandra]

HS14 is not a standard atom type of the gromos 54a7 forcefield and so the
grompp is complaining about it.

You can have a look at this tutorial to get an idea on how to incorporate
non-standard molecules parameters into gromacs
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/02_topology.html

Regards,

Sarath


-- 


On 12 May 2016 at 13:06, Brett <brettliu123 at 163.com> wrote:

> Dear Sarah,
>
>
>
> I use the command grompp, it seems it can recognize all the other
> atomtypes in the ligand.itp.
>
>
> Thus how to solve the special HS14?
>
>
> Brett
>
>
>
>
>
>
>
>
>
> At 2016-05-12 15:03:59, "Sarath Chandra" <sarathchandradantu at gmail.com>
> wrote:
> >What command did you use (pdb2gmx/grompp)? You have to check whether your
> >ligand.itp is referenced in your topol.top for grompp to find the
> atomtypes
> >present in your gro.
> >
> >Regards,
> >
> >Sarath
> >
> >--
> >Sarath Chandra Dantu, PhD, ELS
> >Room No. 606, New BSBE Building
> >Department of Biosciences and Bioengineering
> >Indian Institute of Technology Bombay
> >Powai Mumbai, 400-076, India
> >
> >
> >On 12 May 2016 at 11:40, Brett <brettliu123 at 163.com> wrote:
> >
> >> Dear All,
> >>
> >> By ADP with 54a7 force field, I got a ligand.itp, which contains
> atomtype
> >> HS14. However when I run the md by gromacs with that ligand.itp, it
> told me
> >> the "Atomtype HS14 not found".
> >>
> >> WIll you please tell me how to make gromacs recognize the atomtype HS14?
> >>
> >> Brett
> >> --
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> >>
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