Dear Amber Users,
I am using Amber 14 and have a system that consists of two chains with a
non-covalently bound ligand in the active site of each chain. I would like
to make a distance restraint between the ligand and some active site
residues. And I would like to run this simulation in PMEMD.
How should I write my script since I also have some other restraints
(ntr=1) mentioned?
Here is how my script looks like:
&cntrl
imin=0,
irest=0,
ntx=1,
ntb=1,
cut=10.0,
ntr=1,
ntc=2,
ntf=2,
tempi=0.0,
temp0=300.0,
ntt=3,
gamma_ln=1.0,
ig=1533,
nstlim=10000,
dt=0.001
ntpr=500,
ntwx=500,
ntwr=1000,
ntxo=2,
ioutfm=1,
nmropt=1,
/
the rest of the system restraint
5
RES 1 374
END
END
&wt type='END', /
DISANG=dist.RST
What am I doing wrong?
Looking forward to any advices!
And what should I put in the dist.RST file?
Right now I have multiple lines like that:
&rst restraint = "distance( (5931) (1417) )" /
Best regards,
Karolina Mitusińska
PhD student
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Received on Thu Apr 12 2018 - 07:00:03 PDT
