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AMBER Archive (2007)Subject: AMBER: How to fix two angle but do umberlla sampling for distance?
From: Catein Catherine (askamber23_at_hotmail.com)
Dear Sir/Madam,
I could like to do the umbrella sampling simulation for a drug moving away
I could like to vary the distance betweent the drug and the receptor, i.e.
It is how I write the input files:
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Production MD
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# vary distance restrainst
&rst iat=4,5, r1=0.0, r2=1.0, r3=1.0, r4=100.0, rk2 =60.0, rk3 = 60.,
ATNAM(1)=P,
# fixed angle restrainst
&rst iat=4,5,5 r1=-180.0, r2=180.0, r3=180.0, r4=180.0, rk2 = 1000.0, rk3 =
ATNAM(1)=P,
# fixed torsional angle restraint
ATNAM(1)=P,
=============================================================
However, most of the MD clashed finally or, both angles changed frequently.
It tried to use a smaller rk2 and rk3 values for the fixed angle and
What is the best way to fix two of the angles while changing the distance?
Best regards
Cat
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