Hi,
What is the exact input you are giving to cpptraj? Are you sure you
are using the exact same atoms in cpptraj and in the restraint
definition?
-Dan
On Thu, May 15, 2014 at 11:55 AM, Duggan, Brendan <bmduggan.ucsd.edu> wrote:
> I have been using NMR-derived restraints in a simulated annealing protocol to refine the structure of a non-peptidic small molecule. Distance restraints have been working fine, but the torsion restraints have not. In the sander output the torsion restraint is often reported as violated with a value that does not match what I measure with cpptraj.
>
> My molecule has a carbon-carbon double bond in a trans configuration and I have been trying to restrain the torsion between the protons on either side to ~180o. The restraint I am using is
>
> # 1 PAL H18 1 PAL C18 1 PAL C17 1 PAL H17 160 170 190 200
> &rst
> iat = 53, 3, 4, 34,
> r1 = 160.0, r2 = 170.0, r3 = 190.0, r4 = 200.0,
> rk2 = 2.0, rk3 = 2.0,
> &end
>
> To test the torsion restraint I ran several one step MD runs with just one restraint, the torsion restraint above.
> In the starting co-ordinates the value of this torsion as measured by cpptraj was -179.8360o . After a one step MD run the sander output reports the restraint as violated.
>
> ------------------------------------------------------------------------------
> First atom Last atom curr. value target deviation penalty
> ------------------------------------------------------------------------------
> C18 PLM 1 -- C17 PLM 1: 315.813 190.000 125.813 1.472 t
> Total torsion penalty: 1.472
>
> Using cpptraj to measure the torsion after the one step MD gives a value of 179.9927o.
>
> I see the same behaviour with Amber 11, 12 and 14. Have I defined the restraint incorrectly?
>
> Brendan M. Duggan, PhD
>
> NMR Facility Director and Associate Project Scientist
> Skaggs School of Pharmacy and Pharmaceutical Sciences
> University of California at San Diego
> 9500 Gilman Drive, MC 0684
> La Jolla CA 92093
>
> office phone: (858) 534-8763
> lab phone: (858) 822-7826
> cell phone: (858) 692-2298
> email: bmduggan.ucsd.edu
> http://sopnmr.ucsd.edu
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
-------------------------
Daniel R. Roe, PhD
Department of Medicinal Chemistry
University of Utah
30 South 2000 East, Room 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu May 15 2014 - 11:30:03 PDT
