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 Sat Aug 14 2021 - 13:00:03 PDT
