Hi,
I am trying to simulate hexopyronase using OPLS-AA forcefield
using parameters from the paper:
An improved OPLS?AA force field for carbohydrates, 2002 by Gunsteren.
The set of torsional angle parameters in the paper are given in
Kcal/mol, but because I am using OPLS-AA I would need to convert the
functions into RB-types, right?
Is there a way to convert these functions to RB-types? Or do I convert
them from Kcal/mol to KJ/mol?
Thanks.
Nisha P
Quoting nishap.pa...@utoronto.ca:
Thanks Justin!
Quoting "Justin A. Lemkul" <jalem...@vt.edu>:
nishap.pa...@utoronto.ca wrote:
Hello,
I am trying to simulate hexopyronase using OPLS-AA forcefield
using parameters from the paper:
An improved OPLS?AA force field for carbohydrates, 2002 by Gunsteren.
I was looking through the ffoplsaabon.itp file and there are some
dihedral parameters for hexopyronase. I am not sure what the
comment below means.
Below are extra dihedrals for some special organic molecules.
; Since the atom types are identical to other dihedrals you have to specify
; them explicitly with a define if you happen to simulate this
type of molecule.
How would I mention it in my rtp file? I don't understand ' specify
them explicitly with a define' This is my .rtp for Galactose
See examples in aminoacids.rtp, e.g. ARG.
-Justin
[ GLA ]
[ atoms ]
O opls_180 -0.400 1
C1 opls_195 0.365 2
H1 opls_196 0.100 2
O1 opls_154 -0.683 2
HO1 opls_155 0.418 2
C2 opls_158 0.205 3
H2 opls_176 0.060 3
O2 opls_154 -0.683 3
HO2 opls_155 0.418 3
C3 opls_158 0.205 4
H3 opls_176 0.060 4
O3 opls_154 -0.683 4
HO3 opls_155 0.418 4
C4 opls_158 0.205 5
H4 opls_176 0.060 5
O4 opls_154 -0.683 5
HO4 opls_155 0.418 5
C5 opls_183 0.170 6
H5 opls_185 0.030 6
C6 opls_157 0.145 7
H61 opls_176 0.060 7
H62 opls_176 0.060 7
O6 opls_154 -0.683 7
HO6 opls_155 0.418 7
[ bonds ]
O C1
C1 H1
C1 O1
O1 HO1
C1 C2
C2 H2
C2 O2
O2 HO2
C2 C3
C3 H3
C3 O3
O3 HO3
C3 C4
C4 H4
C4 O4
O4 HO4
C4 C5
C5 C6
C5 O
C6 H61
C6 H62
C6 O6
O6 HO6
--
========================================
Justin A. Lemkul
Ph.D. Candidate
ICTAS Doctoral Scholar
MILES-IGERT Trainee
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
========================================
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the www
interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
--
gmx-users mailing list gmx-users@gromacs.org
http://lists.gromacs.org/mailman/listinfo/gmx-users
Please search the archive at
http://www.gromacs.org/Support/Mailing_Lists/Search before posting!
Please don't post (un)subscribe requests to the list. Use the
www interface or send it to gmx-users-requ...@gromacs.org.
Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
