Hi Dan
Thanks for pointing out the rst command in cpptraj. You were correct. The atom numbers in the restraint did not match what I was trying to define because I had used the wrong PDB file to map atom names to atom numbers. Once I had sorted that out everything ran fine.
Thanks for your help
Message: 5
Date: Thu, 15 May 2014 14:43:40 -0600
From: Daniel Roe <daniel.r.roe.gmail.com>
Subject: Re: [AMBER] torsion restraints not defined properly?
To: AMBER Mailing List <amber.ambermd.org>
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<CAAC0qOZZFBXdOBtgO61_8+LZmkyyhDDhbWH070jSwMX3KHDmoA.mail.gmail.com>
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On Thu, May 15, 2014 at 1:18 PM, Duggan, Brendan <bmduggan.ucsd.edu> wrote:
>
> dihedral H18-H17 .H18 .C18 .C17 .H17 out palmyrolide-1.0.rmd.dihedral
I suspect what may be happening here is that the ordering of your
atoms in the 'dihedral' command does not match what is in the
restraint. You can check this by using the 'rst' command in cpptraj,
e.g.:
rst .H18 .C18 .C17 .H17
If the atom numbers (and order) in the 'iat' line from cpptraj does
not match what you have in your restraint file, that is the issue.
-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
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--
-------------------------
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/
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Received on Tue May 20 2014 - 12:00:03 PDT
