AMBER Archive (2006)

Subject: AMBER: ff02 + POL3 problem !

From: Pradipta Bandyopadhyay (pradipta_at_iitg.ernet.in)
Date: Mon May 15 2006 - 08:53:20 CDT

Hello,

 I am trying to minimize my protein + water system, where protein is
represented by ff02 polarizable force field and the waters are with POL3
force field.

I am using AMBER8 in a dual processor linux machine.

My commands in xleap was

 WAT=PL3
 loadamberparams frcmod.pol3 (this 2 lines are for the waters present in
the PDB file)

 xx = loadpdb xx.pdb
 solvateBox xx POL3BOX 10
 addions2 xx Cl- 6
 saveamberparmpol xx xx.top xx.crd

Xleap saved the top and crd files.

However, when I run a minimization with sander with the following input file:

 &cntrl
   IMIN=1,
   NCYC=100,
   maxcyc=500,
   IPOL=1
   NTR=0
 &end

I get something like this

   NSTEP ENERGY RMS GMAX NAME NUMBER
      1 4.7510E+19 1.0640E+18 2.1944E+20 HE21 30

 BOND = 2218.1501 ANGLE = 827.2355 DIHED = 1791.8357
 VDWAALS = 122128.0995 EEL = ************* HBOND = 0.0000
 1-4 VDW = 723.0874 1-4 EEL = 10994.1160 RESTRAINT = 0.0000
 EPOLAR = ************* ETHREEB = 0.0000
 Dipole convergence: rms = 0.124E+08 temperature = 0.00

   NSTEP ENERGY RMS GMAX NAME NUMBER
     50 1.0814E+20 1.0607E+17 2.1993E+19 HE21 30

 BOND = 3562.1325 ANGLE = 1108.8050 DIHED = 1804.7233
 VDWAALS = 122086.6980 EEL = ************* HBOND = 0.0000
 1-4 VDW = ************* 1-4 EEL = 10796.1395 RESTRAINT = 0.0000
 EPOLAR = ************* ETHREEB = 0.0000
 Dipole convergence: rms = 0.108E+09 temperature = 0.00

and eventually it crashes.

If I replace POL3 with TIP3P (i.e. ff02 + TIP3P), it works fine.

Can someone please help me? Thanks.

 Pradipta

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