Hi,
Are you sure the distance is 3.85? What is the result of the following?
parm complex_wild.prmtop
trajin complex_wild.inpcrd
distance D1 :491.C19 :145.O
run
printdata D1
-Dan
On Sat, Aug 14, 2021 at 3:59 PM Sadaf Rani <sadafrani6.gmail.com> wrote:
>
> Dear Amber user
> Can you please help me to set distance restraint input ( I am using it for
> the first time)
> I want to restraint the distance between a few atoms of ligand and backbone
> amino acids in a protein-ligand complex.
> I am following http://ambermd.org/tutorials/advanced/tutorial4/ tutorial
> and to build 7colum.dist file I am using rst in cpptraj as below:-
> cpptraj
> > parm complex_wild.prmtop
> > reference complex_wild.inpcrd
> rst :491.C19 :145.O reference offset 3.85.0 rk2 10.0 rk3 10.0 out
> 7colum.dist
> run
> quit
>
> The distance between the atoms of the two residues is 3.85 angstrom due to
> which I used offset 3.85
> However, the file I get is as below:-
>
> &rst iat=7992,2344,0
> r1=7.204722, r2=7.704722, r3=7.704722, r4=8.204722, rk2=10.000000,
> rk3=10.000000,
> nstep1=0, nstep2=0,
> &end
> It mentions the distance between r1 and r2 is more than 7 angstroms.
> Is it fine? Could you please help me to understand and set this properly?
> How to set multiple distance restraints between different atoms of these
> residues (here residue 491 and 145).
> I would really appreciate your kind help.
> Thanks in advance.
> Regards
> Sadaf
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Received on Tue Sep 07 2021 - 07:00:03 PDT
