AMBER Archive (2008)

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

From: Yang, Lee-Wei (lwy1_at_pitt.edu)
Date: Wed Jun 04 2008 - 11:27:00 CDT

Dear Ambers,

I have some questions regarding nmode.

I did Newton-Raphson mimization with nmode. The energy is low enough for me to get reasonable normal modes results when using ntrun=1. The first 6 normal modes (that stand for 6 trans/rotation modes) have reasonable eigenvalues very close to zero. Here is part of the output of the 7th mode of protein (1231 atoms):

 ****
    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)?

Before I did Newton-Raphson minimization using nmode, I did thousands of cycles of Steepest-Descend and Conjugated-Gradience (CG) with the GB turned on. I use igb=7, gbsa=1 etc. the script is listed as follows:
&cntrl
imin = 1,
 ntmin=1,
 maxcyc=8000,
 ncyc=2000,
 ntwr=50,
 ntpr=50,
 ntb = 0,
 cut = 50,
 igb=7,
 gbsa=1,
 saltcon=0.2,
 ntr = 0,
&end
&ewald
 eedmeth=5
&end
END

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?

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?

I use Amber 9 with the machine Xeon 2.8GHz x 2cpus, 2GB Memory.

I thank you for any good advice you would like to give.


Lee
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