Re: [AMBER] Help with SMD

From: bharat gupta <>
Date: Tue, 12 Jul 2016 17:02:31 +0900

Hello Amber Users,

I am trying to perform a SMD for my reaction (inversion reaction in
Glycoside Hydrolase) which involves:

(i) a proton transfer from Base residue to the O4 atom glycosidic bond
(ii) breakage of C-O4 bond
(iii) abstraction of proton from nearby water molecule by Acid residue to
charge water for nucleophilic attack on C4 atom.

I was able to perform SMD for the first two step but the energy is way too
high the two reactions. Here's the link for the plots and the output file
from SMD simulation:

Here's the setting files for the SMD:

imin = 0,irest=0,ntx=1,
ntt=3, gamma_ln=1.0,
nstlim=100000, dt=0.0005,
ntpr=50, ntwx=50, ntwr=100,

   output_file = 'smd3.txt'

   output_freq = 100


   type = LCOD ! Linear Combination of Distance # proton transfer step

   i = (8132,7740,7739,7740)

   r = (1.0,-1.0)

   path = (1.25,-1.25)

   harm = (1000.0)

   end variable

    type = DISTANCE ! Distance # glycosidic bond breakage
    i = (8122,8132)
    path = (X,3.0)
    harm = (50.0)
    end variable
end ncsu_smd

Could anybody tell me what could be the reason for such high energy values
for the two steps? I am also confused about keeping the path value for
proton transfer, what does the first and second values indicate in the path

Do I need to perform SMD for step (iii) as well for the entire reaction to
happen or does the abstraction of H from water molecule should occur on its
own, as it is a QM/MM simualtion?

Thanks in advance for your suggestions.

*Best Regards*
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Received on Tue Jul 12 2016 - 01:30:02 PDT
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