AMBER Archive (2002)

Subject: nonpeoridic boundary + mm/gbsa

From: Yongjun Jiang (yjjiang_at_mail.shcnc.ac.cn)
Date: Mon Nov 11 2002 - 06:49:03 CST

Dear all,

 I have calculated binding free energy of a complex with 297 residues receptor and
35 atoms ligand. Three Cl- were added for neutral the system. A 20 A cap of TIP3 water
was added for partially solvated.
First I run 2000 steps of minimization, then 100000 steps for equilibration
and 100000 steps for sample, in the end, mm_gbsa in use.

1) input file for minimization.

-------------------------------------------------------------------------
&cntrl
 imin=1, maxcyc=2000, cut=12, ntpr=20, scee=1.2, ntb=0, nsnb=25, ntmin=2,
&end
-------------------------------------------------------------------------

2) input file for equilibration and sample.
-------------------------------------------------------------------------
&cntrl
 irest=0, ntx=1, tempi=0.0, ntb=0, imin=0, ntt=1, temp0=298.0, taup=.1,
 dtemp=2.0, ntp=0, nstlim =100000, dt=0.002, ntc=2, ntf=2, scee=1.2,
 cut =12.0, nsnb=25, ntpr=100, ntwx=100,
&end
&ewald
 eedmeth=5,
&end
--------------------------------------------------------------------------
The output file for sander-MD is reasonable.
Addition : if eedmeth=4, the system couldn't reach equilibration.
  

3) 50 snapshots from 200-ps were selected excluding the Cl- and water.
 MM-gbsa is used for free energy analyse, but the results for "mm" are
 wrong. for examples. the output flie of complex: md0_com.all.out

-----------------------------------------------------------------------------------
1
 BOND = 740.7613 ANGLE = 2306.6874 DIHED = 1846.5806
 VDWAALS = -2197.5598 EEL = -22133.2883 EGB = -2799.7455
 1-4 VDW = 1116.9826 1-4 EEL = 12097.1717 RESTRAINT = 0.0000
surface area = 11772.7024
2
 BOND = 8963956.6611 ANGLE = 434657.9063 DIHED = 14200.9224
 VDWAALS = ************* EEL = -8219.6179 EGB = -9826.2583
 1-4 VDW = ************* 1-4 EEL = 121.2314 RESTRAINT = 0.0000
surface area = 10079.3468
3
 BOND = 12112917.0404 ANGLE = 416392.2410 DIHED = 14458.5766
 VDWAALS = ************* EEL = -9529.6581 EGB = -9079.9973
 1-4 VDW = ************* 1-4 EEL = 1506.4992 RESTRAINT = 0.0000
surface area = 9999.9357
4
 BOND = 14752382.6272 ANGLE = 403583.8930 DIHED = 13299.6043
 VDWAALS = 17681778.7122 EEL = -7882.3246 EGB = -9762.7571
 1-4 VDW = 6543237.0117 1-4 EEL = 528.1584 RESTRAINT = 0.0000
surface area = 9481.7892
---------------------------------------------------------------------------------
the input file for "MM" analyse
------------------------------------------------------------------------------
File generated by mm_pbsa.pl. Using MM GB MS

 &cntrl
  ntf = 1, ntb = 0, dielc = 1, idecomp= 0, igb = 1, saltcon= 0.0,
  offset = 0.09, extdiel= 80.0, gbsa = 1, surften= 1.0, cut = 99999.0,
  nsnb = 99999, scnb = 2.0, scee = 1.2, imin = 1, maxcyc = 1,
  ncyc = 0,
 &end
---------------------------------------------------------------------------------

How could I do? Thank you in advance.

  
  

                                 
　　　　　　　　　　　　　　Yongjun Jiang
　　　　　　　　　　　　　　yjjiang_at_mail.shcnc.ac.cn
　　　　　　　　　　　　　　　　　2002-11-11