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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Received on Wed Dec 07 2016 - 06:00:04 PST
