Is this sleap or tleap? I didn't think the tleap code had changed outside
of adding SCEE/SCNB sections between 1.4 and 1.5. It's good to know about
this issue, in any case, and is a good reason for upgrading to AmberTools
1.5.
On Fri, May 20, 2011 at 8:04 AM, Thomas Gaillard <
thomas.gaillard.polytechnique.edu> wrote:
> I think maybe you are performing the test with version 1.5 of
> AmberTools? I mentioned that what I describe applies to AmberTools 1.4.
> Indeed comparison of frcmod produced by extractFrcmod.py confirms an
> inconsistency:
>
> gly.frcmod -> multiplicity of 2 for HA2-CA-C-O
> ----------
> H1-CT-C -O 1 0.080 180.000 -3.0 SCEE=1.2 SCNB=2.0
> H1-CT-C -O 1 0.800 0.000 1.0 SCEE=1.2 SCNB=2.0
>
> gly-nhe.frcmod -> multiplicity of 3 for HA2-CA-C-O
> --------------
> H1-CT-C -O 1 0.080 180.000 -3.0 SCEE=1.2 SCNB=2.0
> H1-CT-C -O 1 0.000 0.000 -2.0 SCEE=1.2 SCNB=2.0
> H1-CT-C -O 1 0.800 0.000 1.0 SCEE=1.2 SCNB=2.0
>
> However I think it is preferable to compare directly the prmtop instead
> of converting them to frcmod, as you cannot see the inconsistency
> between HA2-CA-C-O and HA3-CA-C-O parameters in gly-nhe in the frcmod.
>
> 9-6-15-18 = HA2-CA-C-O
> 12-6-15-18 = HA3-CA-C-O
>
> gly.prmtop
> 1 = 0.800 0.000 1.0
> 2 = 0.080 180.000 3.0
> ----------
> 12 6 15 18 1
> 12 6 -15 18 2
> 9 6 15 18 1
> 9 6 -15 18 2
>
> gly-nhe.prmtop
> 3 = 0.800 0.000 1.0
> 4 = 0.080 180.000 3.0
> 5 = 0.000 0.000 2.0
> --------------
> 12 6 15 18 3
> 12 6 -15 18 4
> 9 6 15 18 3
> 9 6 -15 18 5
> 9 6 -15 18 4
>
> Thomas Gaillard
>
> Le Friday 20 May 2011 à 07:16:53AM, Jason Swails a écrit :
> > 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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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
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 - 05:30:07 PDT
