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)?
I know force field (ff14SB) has parameters for Hydroxyproline.
Regards
Tebello
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Received on Wed Dec 07 2016 - 05:30:02 PST
