On 11/03/2015 03:56 PM, Jason Swails wrote:
> On Tue, Nov 3, 2015 at 9:39 AM, Gerald Monard <
> Gerald.Monard.univ-lorraine.fr> wrote:
>
>> Hello,
>>
>> On 11/01/2015 11:52 AM, Jason Swails wrote:
>>> On Sat, Oct 31, 2015 at 1:21 PM, Gerald Monard <
>>> Gerald.Monard.univ-lorraine.fr> wrote:
>>>
>>>> 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., /
>>>>
>>>
>>> What happens if you use the "iat" approach here as well? I've often
>>> observed rather funny behavior with the "natural language" restraints,
>> and
>>> there are a number of peculiar things about that code (for instance -- it
>>> doesn't use the standard mask parser, it implements its own highly
>> limited
>>> version).
>>>
>>>
>>
>> Well, the problem is that I want to use the 'coordinate' mode because I
>> want to restrain the difference between 2 distances. I don't see how to
>> do that with iat.
>> I tried the 'igr' command also (it is mentionned in the manual an
>> unclear relationship between the two), but with no success.
>> Thus I've started to check the code...
>>
>
> It works just fine. To use igr1...8, you need to put "-1" in the iat
> column for that atom. Then you need to use "rstwt" to apply restraint
> weights. For example:
>
> &rst
> iat=-1,-1,-1,-1, igr1=1, 2, 3, 4, 5, igr2=6, 7, 8, 9, 10,
> igr3=11, 12, 13, 14, 15, igr4=16, 17, 18, 19, 20,
> rstwt=1,-1, r1=-10, r2=-5, r3=-5, r4=10, rk1=10, rk2=10,
> /
>
> This defines a coordinate defined by (1)*D1+(-1)*D2, where D1 is the
> distance between the COM of igr1 and igr2, and D2 is the distance between
> the COM of igr3 and igr4. The flat-well potential is defined as per usual
> by the r1, r2, r3, r4 and rk1/2 variables.
>
> This just becomes one of your restraints, and can be used alongside any
> number of other simple restraints.
OK. I got it now.
So, now, instead of 'restraint = coordinate(...)', I can do:
# d2-(d3-d4)
&rst iat = 11,48, 48, 49, 49, 16,
rstwt = 1,-1,1, r0 = 3.2, k0 = 0.0, /
and it works just fine.
Thanks!
G.
>
> All the best,
> Jason
>
--
____________________________________________________________________________
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 Tue Nov 03 2015 - 07:30:02 PST
