Hello,
See the description in the amber manual (same section describing the
generalized distance restraint) regarding making one of the values for iat
negative and defining the corresponding igr variable. For instance, let's
assume that residues 4 and 5 have atom numbers 10-20 and the ligand has atom
numbers 95-100, to define the center of geometry (not COM, because it's not
mass-weighted, according to the manual, but it's close if you neglect
hydrogen atoms)... the restraint file then becomes:
# distance restraint between res4,5 - drug
&rst iat=-1,-1, r1=0.0, r2=10.0, r3=10.0, r4=100.0, rk2 =1.0, rk3 = 1.,
igr1=10,11,12,13,14,15,16,17,18,19,20, igr2=95,96,97,98,99,100 /
Hope this helps,
Jason
On Thu, Aug 12, 2010 at 11:04 PM, Catein Catherine
<askamber23.hotmail.com>wrote:
>
> Dear Sir/Madam,
>
>
>
> I could like to define a distance restraint between residue4+residue5 and
> the drug. I want to define the center of mass for residue4+residue5 and
> drug.
>
>
>
> I know how to define it if I only select one of the atoms from residue4 or
> residue20 or drug(residuenumber 100) as follows:
>
>
>
> # distance restraint
> &rst iat=4,100, r1=0.0, r2=10.0, r3=10.0, r4=100.0, rk2 =1.0, rk3 = 1.,
> iresid=1,
> ATNAM(1)='C1',
> ATNAM(2)='C1' /
>
>
>
> If I want to define the center of mass for the drug, I think I can change
> it to
>
>
>
> # distance restraint
> &rst iat=4,100, r1=0.0, r2=10.0, r3=10.0, r4=100.0, rk2 =1.0, rk3 = 1.,
> iresid=1,
> ATNAM(1)='C1',
> ATNAM(2)='C1', 'H1','H2', 'H3','C2','C3'.....etc for all atoms in the drug
> /
>
>
>
> However, how can I define the center of mass for residue4and20 as one end
> of the distance restraint?
>
>
>
> # distance restraint
> &rst iat=4,20,100, r1=0.0, r2=10.0, r3=10.0, r4=100.0, rk2 =1.0, rk3 = 1.,
> iresid=1,
> ATNAM(1)='C1',...all atoms in residue 4and20.
> ATNAM(2)='C1', 'H1','H2', 'H3','C2','C3'.....etc for all atoms in the drug
> /
>
>
>
> I found the it will mistook as an angle contraint, as I have three entry in
> "iat" now. How can I define which one of them properly?
>
>
> Best regards and many thanks in advance,
>
>
>
> PS. Thanks Jason for my previous question.
>
>
>
> Cat
>
>
>
>
> _______________________________________________
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> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Graduate Student
352-392-4032
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Received on Thu Aug 12 2010 - 20:30:05 PDT
