just to add to what Jason said, I don't think the error message you pasted
is related to using ff99SB vs ff14SB. it seems to be about naming of H
atoms, which does not change between ff99SB and ff14SB. maybe you should
post with a subject about H atom naming in HYP so you might get responses
from people that have done that.
On Wed, Dec 7, 2016 at 8:35 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Wed, Dec 7, 2016 at 8:23 AM, Tsibela German Tebello Mofokeng <
> 1754789.students.wits.ac.za> wrote:
>
> > Dear Amber users
> >
> > I would like to perform a constant pH MD calculation (explicit solvent)
> of
> > a peptide containing hydroxyproline residues using Amber14. I get an
> error
> > message when trying to create the topology and coordinate files by using
> > the following commands:
> >
> > source leaprc.constph
> > >Unitx = loadPDB peptideX.pdb
> > >check Unitx
> >
> > FATAL: Atom .R<HYP 3>.A<HD22 16> does not have a type.
> > FATAL: Atom .R<HYP 3>.A<HD23 17> does not have a type.
> > FATAL: Atom .R<HYP 3>.A<HG 18> does not have a type.
> > FATAL: Atom .R<HYP 6>.A<HD22 16> does not have a type.
> > FATAL: Atom .R<HYP 6>.A<HD23 17> does not have a type.
> > FATAL: Atom .R<HYP 6>.A<HG 18> does not have a type.
> > FATAL: Atom .R<HYP 9>.A<HD22 16> does not have a type.
> > FATAL: Atom .R<HYP 9>.A<HD23 17> does not have a type.
> > FATAL: Atom .R<HYP 9>.A<HG 18> does not have a type.
> > FATAL: Atom .R<HYP 15>.A<HD22 16> does not have a type.
> > FATAL: Atom .R<HYP 15>.A<HD23 17> does not have a type.
> > FATAL: Atom .R<HYP 15>.A<HG 18> does not have a type.
> > FATAL: Atom .R<HYP 18>.A<HD22 16> does not have a type.
> > FATAL: Atom .R<HYP 18>.A<HD23 17> does not have a type.
> > FATAL: Atom .R<HYP 18>.A<HG 18> does not have a type.
> >
> > I then checked the Amber14 reference manual p395, it seem like running
> the
> > following command(source leaprc.constph)loads force field (ff12SB).
> >
> > Which command can I use in Amber14 to load force field (ff14SB) instead
> of
> > (ff12SB)?
> >
>
> ​Actually, leaprc.constph uses ff10, which is the same as ff99SB for
> proteins (not ff12SB). If you need to use ff14SB, I would suggest making a
> copy of leaprc.constph ($AMBERHOME/dat/leap/cmd) in your local directory
> (if you name it "leaprc", tleap will find it automatically).
>
> Then edit that file and have it load leaprc.protein.ff14SB instead of
> oldff/leaprc.ff10.
>
> I recommend against editing leaprc.constph directly (although that will
> work) since then you are technically changing the definition of the
> constant pH force field but you will have no indication in the future that
> anything has changed.
>
> HTH,
> Jason
>
> --
> Jason M. Swails
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>
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Received on Wed Dec 07 2016 - 06:00:05 PST
