Re: [AMBER] Alternative way to do targeted MD

From: Xiaoling Leng <lengxl916.gmail.com>
Date: Thu, 25 Oct 2018 15:43:42 -0400

Thanks. I tried the method you suggested, however there are still give
error says "** NFE-Error ** : Cannot read &colvar namelist!"

Basically, I want to target a protein to the target structure. So the cv is
the Multy_RMSD, the atoms are the Ca atoms for the protein, and the
coordinate of the target is the corresponding Ca atoms' xyz coordinate on
the target structure. I am trying only use linear change of target (so the
RMSD is from X to 0, in the number of steps of this run, correct?)

I followed the format described in the manual section, and don't know why
it call this error.
Attached is the running script (step3.mdin) and cv.in for colvar
definition.




Feng Pan <fpan3.ncsu.edu> 于2018年10月24日周三 下午2:06写道:

> Yes, that's right.
>
> Feng
>
> On Wed, Oct 24, 2018 at 10:55 AM Xiaoling Leng <lengxl916.gmail.com>
> wrote:
>
> > Hello Feng
> >
> > Thank you very much.
> > As I look through 21.6.2, it seems the MULTI_RMSD type for reaction
> > coordinate is the best mimic for RMSD restraint in targeted MD.
> > Am I correct?
> >
> > Thanks.
> >
> > Xiaoling Leng
> >
> > Feng Pan <fpan3.ncsu.edu> 于2018年10月18日周四 下午6:18写道:
> >
> > > Hi, Xiaoling
> > >
> > > You may try the SMD method in NFE module, with the use of RMSD as the
> > > reaction coordinates
> > >
> > > for the details of this usage, you can check the manual section 21.6.3
> > for
> > > the usage of &smd,
> > > and 21.6.2 for the RMSD reaction coordinate
> > >
> > > Feng
> > >
> > > On Thu, Oct 18, 2018 at 2:54 PM Xiaoling Leng <lengxl916.gmail.com>
> > wrote:
> > >
> > > > Hello,
> > > >
> > > > I want to perform a targeted MD simulation on a membrane protein.
> > However
> > > > it is not supported in the pmemd GPU version. May I ask is there any
> > > > alternative way for doing it using GPU? Or like what other types of
> > > > restraints is available in the pmemd can help to simulate a
> transition
> > in
> > > > between structures?
> > > >
> > > > Thanks.
> > > >
> > > > Xiaoling Leng
> > > > _______________________________________________
> > > > AMBER mailing list
> > > > AMBER.ambermd.org
> > > > http://lists.ambermd.org/mailman/listinfo/amber
> > > >
> > >
> > >
> > > --
> > > Feng Pan
> > > PostDoc
> > > 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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> > AMBER.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber
> >
>
>
> --
> Feng Pan
> PostDoc
> 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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Received on Thu Oct 25 2018 - 13:00:03 PDT
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