Re: [AMBER] Creating distaint restaint in Amber

From: Vivien Landre <V.Landre.sms.ed.ac.uk>
Date: Wed, 23 Mar 2011 07:26:30 +0000

Hi,

thank's for your reply earlier!
I tried to run the simulation with the restraint in a separate RST
file. However, I don't think the restraint enters the simulation as I
get the following message in the md.out file

"
    Begin reading energy term weight changes/NMR restraints
  WEIGHT CHANGES:
                          ** No weight changes given **

  RESTRAINTS:
                           ** No restraint defined **

                   Done reading weight changes/NMR restraints
"

I am not sure if I specified the restrain correct in my md.in. The file is
"
  &cntrl
  nmropt=1
  DISANG=dis.RST
&wt type='END'
  imin = 0, irest = 1, ntx = 7,
   ntb = 2, pres0 = 1.0, ntp = 1,
   igb = 0,
   cut = 10,
   ntr = 0,
   ntc = 2, ntf = 2,
   tempi = 300.0, temp0 = 300.0,
   ntt = 3, gamma_ln = 1.0,
   nstlim = 1000000, dt = 0.002

   ntpr = 500, ntwx = 500, ntwr = 5000
  /
"
ad the dis.RST is:
  "
33 LYS NZ 182 GLY C 1.2 2
&rst
  ixpk= 0, nxpk= 0, iat= 562, 2952, r1= 0.7, r2= 1.2, r3= 2, r4=2.5,
  rk2=25.o, rk3=25.0, ir6=1, ialtd=0,
  &end
"
Do you know what could be the problem? Any help is much appreciated!
Thank's
Vivien


Quoting David A Case <case.biomaps.rutgers.edu>:

> On Thu, Mar 10, 2011, Vivien wrote:
>>
>> I want to create one restrain between the C1 of the C-terminal glycine
>> in one molecule and the nitrogen in the lysine group of another
>> molecule. I want the restrain to be between 1.2 and 2. I have already
>> looked through previous entries in the mailing list and as far I as I
>> understand I have to create lines in the restraint file specifying the
>> restraint looking like this:
>>
>> # 34 LYS NZ 183 GLY C 1.2 2
>> &rst
>> ixpk= 0, nxpk= 0, iat= 586, 2969, r1= 0.7, r2= 1.2, r3= 2, r4=2.5,
>> rk2=25.o, rk3=25.0, ir6=1, ialtd=0,
>> &end #
>>
>> ? I want to create the restrain between atom 586 (34 LYS, NZ) and atom
>> 2969 (183 GLY C).
>>
>> However I am not sure how and where to insert the lines in the .rst
>> file?
>
> They go in a separate file, and the name of that file is given on the DISANG
> card in the main mdin file. Also, set nmropt=1 in the &cntrl namelist. See
> examples in Section 6.11 of the Users' Manual.
>
> ...good luck...dac
>
>
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> http://lists.ambermd.org/mailman/listinfo/amber
>
>



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Received on Wed Mar 23 2011 - 00:30:02 PDT
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