AMBER Archive (2004)

Subject: Re: AMBER: Angle parameters in phosphate groups

From: Seongeun Yang (seongeun_at_korea.ac.kr)
Date: Mon Aug 16 2004 - 01:04:16 CDT

Thanks for your interest, Guanglei.

I attached the input and output files of minimization and a resulting structure
of ACE-SEP(-1)-NME minimized by 200 steps with the input parameters.
You may use 'bondbydistance unit' to see the structure of the molecule.
The hydrogen atom of OH group is almost overlapped with other oxygen
atom in the phosphate group, as you can see.
If you have another idea to correct this problem, please let me know.
Thanks again.

Seongeun

-------------------------------------------
 &cntrl
   imin = 1, ntx = 1,
   maxcyc = 500, ntpr = 50,
   dx0 = 0.01, dxm = 0.5, drms = 0.0001,
 &end
 Group input for restrained atoms
  500.0
 RES 4 891
 END
 END
--------------------------------------------------------------------------------
   4. RESULTS
--------------------------------------------------------------------------------

 ---------------------------------------------------
 APPROXIMATING switch and d/dx switch using CUBIC SPLINE INTERPOLATION
 using 5000.0 points per unit in tabled values
 TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
| CHECK switch(x): max rel err = 0.1990E-14 at 2.461500
| CHECK d/dx switch(x): max rel err = 0.7670E-11 at 2.772760
 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 386426
| TOTAL SIZE OF NONBOND LIST = 386426

   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 -7.1305E+03 1.2382E+01 1.6067E+02 OG 14

 BOND = 31.9854 ANGLE = 9.5011 DIHED = 10.8839
 VDWAALS = 858.3322 EEL = -8002.7108 HBOND = 0.0000
 1-4 VDW = 5.6901 1-4 EEL = -44.2219 RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
     50 -9.1035E+03 2.9819E+00 8.5212E+01 PD 15

 BOND = 586.3693 ANGLE = 13.3928 DIHED = 12.3085
 VDWAALS = 1147.7313 EEL = -10808.2603 HBOND = 0.0000
 1-4 VDW = 3.6240 1-4 EEL = -58.6528 RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
    100 -9.5614E+03 2.5695E+00 8.3329E+01 PD 15

 BOND = 641.1457 ANGLE = 25.5212 DIHED = 13.3581
 VDWAALS = 1462.9139 EEL = -11639.1883 HBOND = 0.0000
 1-4 VDW = 3.5012 1-4 EEL = -68.6506 RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
    150 -9.8268E+03 2.0520E+00 5.6447E+01 PD 15

 BOND = 680.9148 ANGLE = 31.4140 DIHED = 13.5916
 VDWAALS = 1652.2477 EEL = -12126.2005 HBOND = 0.0000
 1-4 VDW = 3.1010 1-4 EEL = -81.8714 RESTRAINT = 0.0000

   NSTEP ENERGY RMS GMAX NAME NUMBER
    200 -1.2331E+04 1.8339E+03 1.0889E+05 OE2 17

 BOND = 1043.4708 ANGLE = 123.8957 DIHED = 14.1976
 VDWAALS = 1704.9043 EEL = -12095.1581 HBOND = 0.0000
 1-4 VDW = 3.5410 1-4 EEL = -3125.9904 RESTRAINT = 0.0000
---------------------------------------------------------------------------------------

ATOM 1 HH31 ACE 1 16.987 12.760 18.074
ATOM 2 CH3 ACE 1 16.230 13.463 17.624
ATOM 3 HH32 ACE 1 15.272 13.143 17.942
ATOM 4 HH33 ACE 1 16.311 13.432 16.582
ATOM 5 C ACE 1 16.465 14.793 18.209
ATOM 6 O ACE 1 17.331 14.970 19.195
ATOM 7 N SE1 2 15.923 15.951 17.637
ATOM 8 H SE1 2 15.281 15.719 16.844
ATOM 9 CA SE1 2 16.061 17.225 17.980
ATOM 10 HA SE1 2 16.172 17.342 18.948
ATOM 11 CB SE1 2 17.556 17.708 17.408
ATOM 12 HB2 SE1 2 18.182 17.011 17.613
ATOM 13 HB3 SE1 2 17.388 17.968 16.368
ATOM 14 OG SE1 2 17.929 18.954 18.171
ATOM 15 PD SE1 2 19.496 19.342 17.986
ATOM 16 OE1 SE1 2 20.316 18.507 18.713
ATOM 17 OE2 SE1 2 19.733 20.351 17.316
ATOM 18 OE3 SE1 2 19.577 20.546 17.869
ATOM 19 HE3 SE1 2 19.728 20.376 17.308
ATOM 20 C SE1 2 14.977 18.082 17.441
ATOM 21 O SE1 2 14.097 17.612 16.742
ATOM 22 N NME 3 14.934 19.417 17.847
ATOM 23 H NME 3 15.826 19.726 18.280
ATOM 24 CH3 NME 3 14.002 20.437 17.496
ATOM 25 HH31 NME 3 13.177 20.043 16.857
ATOM 26 HH32 NME 3 13.563 20.762 18.409
ATOM 27 HH33 NME 3 14.463 21.282 16.985
ATOM 28 Na+ Na+ 4 22.297 17.610 18.398
---------------------------------------------------------------

----- Original Message -----
From: "Guanglei Cui" <cuigl_at_csb.sunysb.edu>
To: <amber_at_scripps.edu>
Sent: Sunday, August 15, 2004 11:08 PM
Subject: Re: AMBER: Angle parameters in phosphate groups

> Hi, Seongeon
>
> It'd be nice to have a few lines of your min output and other essential
> files, such as parmtop and inpcrd, to see what's happened.
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