Thanks, Carlos, I will read these papers.
On Aug 18, 2017 3:41 PM, "Carlos Simmerling" <carlos.simmerling.gmail.com>
wrote:
this isn't really directly related to your question, but for defining the
base flipping center of mass groups you might want to read the following
article where we examined the approach you are using and found
difficulties, at least for our systems.
An Improved Reaction Coordinate for Nucleic Acid Base Flipping Studies
Song, K., Campbell, A., Bergonzo, C., de los Santos, C., Grollman, A.,
Simmerling, C.
Journal of Chemical Theory and Computation, 2009, 5 (11), 3105-3113
DOI: 10.1021/ct9001575
for obtaining free energy profiles of flipping, including 2D mapping with
the glycosidic angle, you could look at these examples:
Energetic Preference of 8-oxoG Eversion Pathways in a DNA Glycosylase
Bergonzo, C., Campbell, A., de los Santos, C., Grollman, A and Simmerling,
C., Journal of the American Chemical Society, 2011, 133, 14504–14506
DOI: 10.1021/ja205142d
Active destabilization of base pairs by a DNA glycosylase wedge initiates
damage recognition
Kuznetsov, N. A., Bergonzo, C., Campbell, A. J., Li, H., Mechetin, G. V.,
de los Santos, C., Grollman, A. P., Fedorova, O. S., Zharkov, D. O.,
Simmerling, C., Nucleic Acids Research, 2015, 43 (1), 272-281
DOI: 10.1093/nar/gku1300
A Dynamic Checkpoint in Oxidative Lesion Discrimination by
Formamidopyrimidine–DNA Glycosylase
Li, H., Endutkin, A., Bergonzo, C., Grollman, A.; Campbell, A., de los
Santos, C., Zharkov, D., Simmerling, C., Nucleic Acids Research,
2015,44(2), 683-94
DOI:10.1093/nar/gkv1092
DNA Deformation-Coupled Recognition of 8‑Oxoguanine: Conformational Kinetic
Gating in Human DNA Glycosylase
Haoquan Li, Anton V. Endutkin, Christina Bergonzo, Lin Fu, Arthur Grollman,
Dmitry O. Zharkov, and Carlos Simmerling, Journal of the American Chemical
Society, 2017, 139 (7), 2682-2692
DOI: 10.1021/jacs.6b11433
On Thu, Aug 17, 2017 at 10:22 PM, Chunli Yan <utchunliyan.gmail.com> wrote:
> Hi, Feng,
>
> I defined two colvars: Pseudo-torsion and Glycosidic torsion to find path
> for base flipping in DNA. My initial centers are the following:
>
> Frame Pseudo #Frame Glycosidic
>
> 1 -22.9834 1 -130.0178
>
> 2 -1.8113 2 -105.8328
>
> 3 17.1431 3 -87.6128
>
> 4 18.1844 4 -59.2702
>
> 5 28.7286 5 -113.0601
>
> 6 37.1831 6 -123.4999
>
> 7 48.8440 7 -108.6611
>
> 8 60.1785 8 -151.3533
>
> 9 66.9365 9 -120.1098
>
> 10 68.9553 10 -137.1430
>
> 11 81.9498 11 -118.3375
>
> 12 122.5714 12 -154.9839
>
> 13 127.7331 13 -132.3430
>
> 14 145.1492 14 -146.8632
>
> 15 125.7844 15 -112.9243
>
> 16 144.7185 16 -134.7721
>
> 17 153.0255 17 -146.5084
>
> 18 167.3042 18 -127.8211
>
> 19 175.7482 19 -139.4776
>
> 20 179.6935 20 61.0230
>
> But after I simulate it using string methods, I have 20 images, 20 repeats
> per image and 300 iterations per repeats. I found some values changed from
> positive to negative, such as the first iterations below:
>
> center of image 1 : 20 -0.40085575 -2.39713917
>
> center of image 2 : 20 -0.04998067 -1.95821022
>
> center of image 3 : 20 0.12711176 -1.43258465
>
> center of image 4 : 20 0.22593965 -1.67138273
>
> center of image 5 : 20 0.46420370 -2.12574684
>
> center of image 6 : 20 0.82577461 -2.03805261
>
> center of image 7 : 20 1.16971343 -2.49178907
>
> center of image 8 : 20 1.24398057 -2.30938805
>
> center of image 9 : 20 1.65712794 -2.21598440
>
> center of image 10 : 20 2.08806127 -2.58816551
>
> center of image 11 : 20 2.30771252 -2.34113196
>
> center of image 12 : 20 2.14452605 -2.12182890
>
> center of image 13 : 20 2.50822092 -2.44579490
>
> center of image 14 : 20 2.82097066 -2.25111436
>
> center of image 15 : 20 -3.03275023 -2.29560698
>
> center of image 16 : 20 -3.05625542 -2.37193291
>
> center of image 17 : 20 -3.07979668 -2.77849152
>
> center of image 18 : 20 -3.10334797 1.34943046
>
> center of image 19 : 20 -3.12688318 1.11151901
>
> center of image 20 : 20 3.13280899 1.05163244
>
> Please find attached two torsions I defined and final string plot.
>
>
>
> Best,
>
>
> *Chunli*
>
>
>
> On Thu, Aug 17, 2017 at 6:48 PM, Feng Pan <fpan3.ncsu.edu> wrote:
>
> > Hi, Chunli
> >
> > String method can only give the least free energy path in the phase
> space,
> > cannot
> > give the whole landscape of free energy.
> >
> > To get the PMF, you can use umbrella sampling, or the ABMD method by
> &abmd
> > module,
> > you can check the manual for details.
> >
> > Best
> > Feng
> >
> > On Thu, Aug 17, 2017 at 1:42 AM, Chunli Yan <utchunliyan.gmail.com>
> wrote:
> >
> > > Hello,
> > >
> > > After I finished the simulation by using string methods, I got a lists
> of
> > > output file for each image (mdcrd*, rst*, stsm* and so on). In amber
> > > manual:
> > >
> > > When you get the biasing potential (*.nc file), you can always use
> the
> > > nfe-umbrella-slice utility to access
> > >
> > > its content and get a friendly-written ASCII file from which one can
> > obtain
> > > the free energy map. The output
> > >
> > > is the free energy value, which is the opposite of the biasing
> potential
> > (
> > > f = U (units kcal*=*mol )). The
> > >
> > > nfe-umbrella-slice utility has been included in AmberTools.
> > >
> > >
> > > Usage: nfe-umbrella-slice [options] bias_potential.nc
> > >
> > >
> > > I am wondering how to compute free energy along the image. How to get
> the
> > > biasing potential.
> > >
> > >
> > > Thanks,
> > >
> > >
> > > Best,
> > >
> > >
> > > *Chunli*
> > > _______________________________________________
> > > AMBER mailing list
> > > AMBER.ambermd.org
> > > http://lists.ambermd.org/mailman/listinfo/amber
> > >
> >
> >
> >
> > --
> > Feng Pan
> > Ph.D. Candidate
> > North Carolina State University
> > Department of Physics
> > Email: fpan3.ncsu.edu
> > _______________________________________________
> > AMBER mailing list
> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
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>
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Received on Fri Aug 18 2017 - 15:00:03 PDT
