AMBER Archive (2004)

Subject: Re: AMBER: Bad contacts

From: bybaker_at_itsa.ucsf.edu
Date: Wed Jun 09 2004 - 15:30:38 CDT

Hello, Carlos:

The structure-0 was first subjected to minimization, and .pdb file
(Structure-1) was saved from .rst file. The structure-1 was viewed at
SwissPSB Viewer. Several residues, most are HID, were identified to make
‘aa clashing’. Structure-1 was manually modified to remove the bad
contacts. The resulted structure is called structure-2. This structure
was then to subjected energy minimization run for 1000 steps in Sander.
After the run, there is no significant change at energy level, and the
bad contacts those make ‘aa clashing’, HID162 and LYS172, are still
there. There is changes of GMAX, from ND1 3342 to CG 3341, but they
don’t refer to either HID162 or LYS172.

Sorry for the confuse. The follow is the result from sander run.

Regards

Bo Yang

-----Start-----

guanine.10% less run3min.out

Here is the input file:
 
Minimization of entire molecular system
 &cntrl
  imin=1, ncyc=200, maxcyc=1000, ntb=0,
 &end

4. RESULTS
--------------------------------------------------------------------------------

 ---------------------------------------------------

     eedmeth=4: Setting switch to one everywhere

 ---------------------------------------------------
| Local SIZE OF NONBOND LIST = 455102
| TOTAL SIZE OF NONBOND LIST = 455102

   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 -3.1375E+03 4.4981E+00 7.7926E+01 ND1 3342

 BOND = 193.2530 ANGLE = 704.6748 DIHED = 1889.6293
 VDWAALS = -827.3288 EEL = -15253.8509 HBOND = 0.0000
 1-4 VDW = 904.4166 1-4 EEL = 9251.6560 RESTRAINT = 0.0000

NSTEP ENERGY RMS GMAX NAME NUMBER
   1000 -3.0996E+03 3.4211E+00 3.7562E+01 CG 3341

 BOND = 181.8019 ANGLE = 683.3846 DIHED = 1887.3142
 VDWAALS = -827.1378 EEL = -15177.3605 HBOND = 0.0000
 1-4 VDW = 901.6250 1-4 EEL = 9250.7928 RESTRAINT = 0.0000

------End-----
    -------------------------------------------------------

On Wed, 9 Jun 2004 14:56:09 -0400 "Carlos Simmerling" wrote:

> this doesn't make sense- you minimized the structure for 1000 steps
> and the energy did not change?
> carlos
>
> >This structure is
> > subjected to energy minimization for 1000 steps in Sander (Amber7), but
> > no change is made in either energy level or structure geometry.
> These two
> > residues still make 'aa clashing' in SwizzPDB Viewer.
> >
> >
>
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