AMBER Archive (2008)

Subject: RE: AMBER: NMODE units and hrmax value for Langevine modes

From: Yang, Lee-Wei (lwy1_at_pitt.edu)
Date: Wed Jun 04 2008 - 22:55:45 CDT

Thank you for the useful reply Dave. I wonder if there is a 'ok' hrmax value (for all the heavy atoms) that I can use to get a first approximation.
Also, what is the value 0.2 for hydrogen? means 20% of its surface area being covered by solvent? therefore the value of hrmax has its maxima unity and minimum zero? It will be very kind of you to forward me a pointer regarding this. Thank you in advance.

Lee
________________________________________
$B4s7o<T(B: owner-amber_at_scripps.edu [owner-amber_at_scripps.edu] $BBeI=(B David A. Case [case_at_scripps.edu]
$B4s7oF|4|(B: 2008$BG/(B6$B7n(B5$BF|(B $B>e8a(B 02:30
$BZ_at_7o<T(B: amber_at_scripps.edu
$B<g;](B: Re: AMBER: NMODE units and hrmax value for Langevine modes

On Wed, Jun 04, 2008, Yang, Lee-Wei wrote:
>
> ****
> 7 3.85484
> -0.00012 -0.00404 0.00481 -0.00050 -0.00464 0.00449 0.00005
> -0.00447 0.00525 0.00030 -0.00331 0.00529 -0.00078 -0.00334
> 0.00373 -0.00138 -0.00422 0.00304 -0.00039 -0.00270 0.00419
> -0.00019 -0.00231 0.00373 -0.00050 -0.00293 0.00454 -0.00015
> -0.00231 0.00481 0.00024 -0.00175 0.00543 -0.00075 -0.00273
> 0.00527 0.00045 -0.00208 0.00384 0.00030 -0.00184 0.00489
> 0.00072 -0.00121 0.00618 -0.00087 -0.00248 0.00506 0.00102
> -0.00168 0.00406 -0.00113 -0.00204 0.00306 -0.00066 -0.00220
> ........................................................................
>
> I just want to make sure that I understand these data correctly. So the
> number "3.85484" is the frequency in the unit of cm^-1? and the values below
> that (read from left to right and then up to down) are the non-mass weighted
> eigenvector values (mass-weighted eigenvector divided by square root of mass
> of each atom)?

I believe this is correct. When I use such vectors (from QM or MM programs),
I generally include a check on the orthogonality and normalization criteria,
to be sure that my program (and I) understand what the numbers mean.

> However, when I switch to nmode's Newton-Raphson (NR), the energy of the
> configuration computed by CG is very different from that computed by
> NR. I guess it is due to the GB part. Can one use nmode to do NR using
> solvation(by GB model)-included energy? or NAB can help us do that?

Yes: you should use NAB for this. The nmode program doesn't know about GB.

>
> My last question is regarding the hrmax flag for assigning hydrodynamic
> radii of atoms, which is needed in calculation of Langevine modes (using
> nmode). Just to get a first approximation, what number should I use for my
> heavy atoms (if 0.2 is used for hydrogen atoms). In AmberTool manual, the
> NAB session, it is said that I may acquire some molecular surface packages
> to compute such radii. What package will you recommand to use? Also the
> format of the file 'expfile' is not so clear to me. If used, how should I
> assign the flag? something like hrmax='expfile'? or I just simply put that
> file in the working directory?

You can use the "-e" flag to set the name of the expfile; the default is
"expfil'. The format of the file is a namelist called &expos that contains a
vector of natom entries called "expr". See setgam.f for details. Again, NAB
might be a better choice: we will be phasing out nmode in future versions.

...good luck...dac

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