# Re: [AMBER] &rst + distance + coordinate restraint

From: Daniel Roe <daniel.r.roe.gmail.com>
Date: Mon, 2 Nov 2015 10:09:06 -0700

Hi,

This isn't a direct answer to your question, but if you just want to
make restraints using mask syntax you could use the 'rst' command from
cpptraj, e.g.

rst :1.C :3.O r1 <r1> r2 <r2> r3 <r3> r4 <r4> rk2 <rk2> rk3 <rk3> out file.rst
rst ... out file.rst

etc. Can also be used to create angle (3 masks) and torsion (4 masks)
restraints.

-Dan

On Sat, Oct 31, 2015 at 11:02 AM, Gerald Monard
<Gerald.Monard.univ-lorraine.fr> wrote:
> Hello,
>
> There's something that I don't understand with using restraints in
> sander. I want to do umbrella sampling for a reaction. For that, I
> define 3 distances between couples of atoms: d2, d3 and d4. I want to
> restraint a combination of d2/d3/d4 but also to output individual values.
> To do so, I have created the following DISANG file:
> """
> # d2
> &rst restraint = "distance(:1.C,:3.O)", r0 = 3.2, k0 = 0., /
> # d3
> &rst restraint = "distance(:3.O,:3.H1)", r0 = 1.0, k0 = 0., /
> # d4
> &rst restraint = "distance(:3.H1,:2.OP2)", r0 = 1.8, k0 = 0., /
> # d3-d4
> &rst restraint =
> "coordinate(distance(:3.O,:3.H1),1.0,distance(:3.H1,:2.OP2),-1.0)",
> r0 = 3.2, k0 = 0., /
> # d2-(d3-d4)
> &rst restraint = "coordinate(distance(:1.C,:3.O), 1.0,
> distance(:3.O,:3.H1), -1.0, distance(:3.H1,:2.OP2), 1.0)",
> r0 = 3.2, k0 = 0., /
> """
>
> If I run sander (AmberTools15), it crashes with:
> """
> Here are comments from the DISANG input file:
> # d2
>
> Error: Invalid atom or grouping specified in restraint.
> restraint = "distance( :1.C :3.O )"
> """
>
> What is surprising is that if I comment all &rst except one, all
> individual restraints are OK (i.e., sander run correctly). If I use
> together only d2, d3 and d4 for restraints, no problem also. But any
> combination of 'coordinate' with a distance or both 'coordinate'
> restraints together give an error with sander.
>
> Any idea?
>
> Gerald.
>
>
> --
> ____________________________________________________________________________
>
> Prof. Gerald MONARD
> SRSMC, Université de Lorraine, CNRS
> Boulevard des Aiguillettes B.P. 70239
> F-54506 Vandoeuvre-les-Nancy, FRANCE
>
> e-mail : Gerald.Monard.univ-lorraine.fr
> tel. : +33 (0)383.684.381
> fax : +33 (0)383.684.371
> web : http://www.monard.info
>
> ____________________________________________________________________________
>
>
> _______________________________________________
> 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 307
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 Mon Nov 02 2015 - 09:30:02 PST
Custom Search