Note that you can use the 'rst' command in cpptraj to generate
distance/angle/dihedral restraints using mask expressions, e.g.:
rst :1-79 :80-158 r1 0 r2 10 r3 10 r4 100 rk2 1 rk3 1
This command can also be used with a reference structure to
automatically set r1-4, optionally subject to a width and offset. See
the manual for more details.
-Dan
On Fri, Jun 6, 2014 at 6:20 AM, Jason Swails <jason.swails.gmail.com> wrote:
> On Fri, Jun 6, 2014 at 3:11 AM, whb <wwwhbpt.gmail.com> wrote:
>
>> Dear amber users：
>>
>> I want to know that the dimer-to-monomer transition of a protein
>> by
>> using CPHMD simulations and the umbrella sampling method to obtain the
>> potential of mean force(PMF) as a function of the distance between the
>> centers of mass of the two monomers.
>>
>> Now I have a little trouble writing the DISANG file. Monomer has 79AAs. I
>> don’t know how to acquire the original distance between the two monomers,
>> and don’t know how to define the distance between two residues. I tried to
>> read the manual, but still got a little problems. I hope someone could help
>> me finish the DISANG file. And tell me how to define the variable number.
>>
>> &rst
>>
>> iat=-1,-1,
>>
>> r1=0.0, r2=10.0, r3=10.0, r4=100.0,
>>
>> rk2 =1.0, rk3 = 1,
>>
>> iresid=1,
>>
>>
>> igr1=1-79,
>>
>
> You cannot specify an atom range in a Fortran namelist. You must specify
> each atom your want in your group explicitly. To avoid adding a full 79
> atoms to each group, see if you can select a subset that will still give
> you basically the same center of geometry.
>
> Other than these errors that were easy to detect, it's impossible to
> provide help when we don't know what you did, what error you got, or what
> you mean by "define the variable number". Please try and be specific and
> report exactly what you tried and the messages you got (do _not_ paraphrase
> or summarize).
>
> HTH,
> Jason
>
> --
> Jason M. Swails
> BioMaPS,
> Rutgers University
> Postdoctoral Researcher
> _______________________________________________
> 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 201
Salt Lake City, UT 84112-5820
http://home.chpc.utah.edu/~cheatham/
(801) 587-9652
(801) 585-6208 (Fax)
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Received on Fri Jun 06 2014 - 07:00:03 PDT
