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
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 19 2011 - 20:30:02 PDT
