Hi Jason,
You are right that the problem does not occur with your sequences. To
reproduce the problem I describe, you have to build a GLY-XXX sequence
and compare to isolated GLY, like this:
source leaprc.ff99SB
l = sequence { GLY }
k = sequence { GLY NHE }
saveamberparm l gly.parm7 gly.rst7
saveamberparm k gly-nhe.parm7 gly-nhe.rst7
quit
You will then see that the HA2-CA-C-O dihedral (numbered 9-6-15-18 in the
prmtop) has a multiplicity of 3 in gly-nhe while 2 in gly. Below are the
interesting parts of the prmtop.
I think that even if the sequences are "unphysical", the assignment of
dihedrals by leap should be consistent.
The version I used is the amber11-with-patches git branch so I think
this corresponds to AmberTools 1.4.
gly.parm7
---------
%FLAG ATOM_NAME
%FORMAT(20a4)
N H CA HA2 HA3 C O
%FLAG DIHEDRAL_FORCE_CONSTANT
%FORMAT(5E16.8)
8.00000000E-01 8.00000000E-02 0.00000000E+00
%FLAG DIHEDRAL_PERIODICITY
%FORMAT(5E16.8)
1.00000000E+00 3.00000000E+00 2.00000000E+00
%FLAG DIHEDRAL_PHASE
%FORMAT(5E16.8)
0.00000000E+00 3.14159400E+00 0.00000000E+00
%FLAG DIHEDRALS_INC_HYDROGEN
%FORMAT(10I8)
12 6 15 18 1 12 6 -15 18 2
9 6 15 18 1 9 6 -15 18 2
3 0 6 9 3 3 0 6 12 3
3 0 6 15 3
gly-nhe.parm7
-------------
%FLAG ATOM_NAME
%FORMAT(20a4)
N H CA HA2 HA3 C O N HN1 HN2
%FLAG DIHEDRAL_FORCE_CONSTANT
%FORMAT(5E16.8)
2.00000000E+00 2.50000000E+00 8.00000000E-01 8.00000000E-02 0.00000000E+00
4.50000000E-01 1.58000000E+00 5.50000000E-01 0.00000000E+00 1.05000000E+01
1.00000000E+00
%FLAG DIHEDRAL_PERIODICITY
%FORMAT(5E16.8)
1.00000000E+00 2.00000000E+00 1.00000000E+00 3.00000000E+00 2.00000000E+00
1.00000000E+00 2.00000000E+00 3.00000000E+00 4.00000000E+00 2.00000000E+00
2.00000000E+00
%FLAG DIHEDRAL_PHASE
%FORMAT(5E16.8)
0.00000000E+00 3.14159400E+00 0.00000000E+00 3.14159400E+00 0.00000000E+00
3.14159400E+00 3.14159400E+00 3.14159400E+00 0.00000000E+00 3.14159400E+00
3.14159400E+00
%FLAG DIHEDRALS_INC_HYDROGEN
%FORMAT(10I8)
18 15 21 24 1 18 15 -21 24 2
18 15 21 27 1 18 15 -21 27 2
12 6 15 18 3 12 6 -15 18 4
12 6 15 21 5 9 6 15 18 3
9 6 -15 18 5 9 6 -15 18 4
9 6 15 21 5 6 15 21 24 2
6 15 21 27 2 3 0 6 9 5
3 0 6 12 5 3 0 6 15 5
15 24 -21 -27 11
Thomas Gaillard
Le Thursday 19 May 2011 à 11:21:19PM, Jason Swails a écrit :
> I do not see this. I used the following script:
>
> source leaprc.ff99SB
>
> l = sequence {ACE ALA GLY NHE}
> k = sequence {ACE ALA GLY ALA NHE}
>
> saveamberparm l nhe.parm7 nhe.rst7
> saveamberparm k gly.parm7 gly.rst7
>
> quit
>
> Then I used "extractFrcmod.py" to create frcmod files from nhe.parm7 and
> gly.parm7 (this script just extracts the parameters from these prmtop files
> and puts it into "frcmod" format).
>
> The two frcmod files are identical (as they should be). Can you give me an
> instance where this is not the case for you?
>
> All the best,
> Jason
>
> On Thu, May 19, 2011 at 8:16 PM, Thomas Gaillard <
> thomas.gaillard.polytechnique.edu> wrote:
>
> > When comparing prmtop files created by leap (AmberTools 1.4 version) for
> > GLY and GLY-NHE (where GLY is GLY and not NGLY) with the ff99SB force
> > field, I found some inconsistencies in the dihedrals:
> >
> > The HA2-CA-C-O dihedral has a multiplicity of 3 in GLY-NHE whereas
> > the same dihedral in GLY has a multiplicity of 2, and the HA3-CA-C-O
> > dihedral in GLY-NHE has a multiplicity of 2.
> >
> > This is of course inconsistent because: 1) the HA2-CA-C-O dihedral
> > belongs to the GLY residue and its parameters should not be affected by
> > the presence of the NHE residue; 2) as HA2 and HA3 atoms are equivalent,
> > HA2-CA-C-O and HA3-CA-C-O dihedrals should have the same parameters.
> >
> > It appears that the multiplicity of 2 for the HA2-CA-C-O dihedral
> > corresponds to the expected H1-CT-C-O parameters in parm99.dat:
> >
> > H1-CT-C -O 1 0.80 0.0 -1. Junmei et al, 1999
> > H1-CT-C -O 1 0.08 180.0 3. Junmei et al, 1999
> >
> > while the multiplicity of 3 corresponds to the addition of the wild-card
> > parameter:
> >
> > X -C -CT-X 6 0.00 0.0 2. JCC,7,(1986),230
> >
> > I was wondering if this problem is known, and what could explain the
> > inconsistency in the assignment of parameters for this type of dihedral.
> > Note that the problem also occurs with other GLY-XXX sequences.
--
Thomas Gaillard
Maître de conférences
Laboratoire de Biochimie
Ecole Polytechnique
91128 Palaiseau cedex
tel: +33 1 69 33 48 62
fax: +33 1 69 33 49 09
thomas.gaillard.polytechnique.edu
http://bioc.polytechnique.fr/~gaillard
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Received on Fri May 20 2011 - 04:00:02 PDT
