As a follow-up, I can partially solve the problem using "iat":
# d2
&rst iat = 11, 48, r0 = 3.2, k0 = 0., /
# d3
&rst iat = 48, 49, r0 = 3.2, k0 = 0., /
# d4
&rst iat = 49, 16, 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., /
But I still can't add multiple "&rst restraint=[...]" commands.
I haven't seen such restriction in the manual, but may be I haven't
search correctly.
Gerald.
On 10/31/2015 06:02 PM, Gerald Monard 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
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Received on Sat Oct 31 2015 - 10:30:04 PDT
