AMBER Archive (2006)

Subject: RE: AMBER: ff02 + POL3 problem !

From: Yong Duan (duan_at_ucdavis.edu)
Date: Mon May 15 2006 - 11:15:02 CDT

Pradipta,

The problem might have been caused by one or more water hydrogen atoms
moving too close to oxygens. This can happen since van der Waals radii of
POL3 hydrogens are zero (so are those of other water models). These water
models were developed based on the fixed geometry. Therefore, when they are
used in simulation, their bonds have to be constrained. You need to set
NTC=2 to turn on SHAKE, if you did not do so. The default is ntc=1. I'd
suggest that you change src/sander/mdread.f, line 164, "ntc = 1" to "ntc =
2" just to avoid similar problem from happening again.

yong

> -----Original Message-----
> From: owner-amber_at_scripps.edu
> [mailto:owner-amber_at_scripps.edu] On Behalf Of Pradipta Bandyopadhyay
> Sent: Monday, May 15, 2006 6:53 AM
> To: amber_at_scripps.edu
> Subject: AMBER: ff02 + POL3 problem !
>
>
>
> 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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