I still don't see the issue with those sequences. Create frcmod files using
extractFrcmod.py and see that each dihedral (or any parameter) that is
defined in both topology files is defined exactly the same...
HTH,
Jason
On Fri, May 20, 2011 at 6:47 AM, Thomas Gaillard <
thomas.gaillard.polytechnique.edu> wrote:
> 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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>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Fri May 20 2011 - 04:30:03 PDT
