Thank you a lot
On 7 December 2016 at 15:38, Carlos Simmerling <carlos.simmerling.gmail.com>
wrote:
> 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
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
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Received on Wed Dec 07 2016 - 06:00:06 PST
