Re: [AMBER] Umbrella Sampling

From: bharat gupta <>
Date: Sat, 2 Jul 2016 22:19:45 +0900

Hello Amber Users,

I am looking for the answers related to my Umbrella Sampling study. I have
already posted this query in the forum but nobody has responded so far. So,
I am posting it again with the hope of getting some answers.

I am studying a simultaneous proton transfer, bond breakage and nucleophilic
attack (by water molecule), using US approach for which I had already
performed 5ns QM/MM simulation.

All three reactions takes places in a single step (Inversion mechanism for
Glycoside hydrolase). Now, I am confused in defining the restraint

I have selected 4 Reaction Coordinates:

1. RC1: Proton transfer from Base residue to leaving group
     OE1-HE1 -> C----O4 (this glycosidic bond breaks and HE1 is transferred
to O4 )
    So, the reaction coordinate for this reaction is difference in distance
between OE1-HE1 and O4--HE1.

2. RC2: Glycosidic bond breakage:
    C-----O4 -> C O4. The reaction coordinate for this reaction is the
distance between C and O4

3. RC3: Nucleophilic attack by water:
     H(i)O(w)H(w) [this is nucleophilic water] ---- C (anomeric carbon of
the broken glycosidic bond). The reaction coordinate for this reaction is
the distance between C and O(w).

4. RC4: Proton transfer from water (H(i)) to Acid Residue
     H(i)O(w)H(w) -- OD1 (Acid residue). The reaction coordinate for this
step is difference in distance between O(w)-H(i) and OD1-H(i).

For the RC2, I have made the following restraint file:
# distance restraint
 &rst iat=8122,8132 r1=0, r2=1.8, r3=1.8, r4=5, rstwt=1,-1, rk2 = 500.0,
rk3 = 500.0, /

I have increased the the value for r2 & r3 by 0.2 and upto 3.4. I am not
able to understand what should be the value for r1 and r4 ? Could anyone
pls comment on it and explain it briefly?

I also not able to understand how to make the restraint file for difference
in distances between two set of atoms, as in case of RC4 and RC1. I would
be helpful for me if somebody explains it too with an example.

I also want to visualize all the four reaction steps so which trajectory
files from all the four RCs I should see?

Since I am new to US, it would be a great help if somebody can guide me
through this.

*Best Regards*
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Received on Sat Jul 02 2016 - 06:30:02 PDT
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