Hello Yong,
Thanks a lot for your help.
I did with shake on but still the problem remains
I tried the following protocol
(1) first IPOL=0 and shake off
(2) then IPOL=1 and shake off
(3) then IPOL=1 and shake on
however, whenever I turn on shake with IPOL=1, it is stopping with
'LINMIN FALIURE'.
I tried one MD with shake off (from the minimized geometry of IPOL=1 and
shake=off) - it crashes in 50 steps (since, some parts of the system is
getting large forces).
I would appreciate any suggestion.
regards,
Pradipta
p.s. one thing is not clear - it seems we must set NTC=2 for fixing rigid
water models. what happens if someone does NTC=1 in MD for TIP3P+protein -
does AMBER by default fix the rigid water models? Otherwis if models like
TIP3P is not kept rigid then it is no longer a TIP3P model strictly
speaking.
>
> 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.scripps.edu
>> [mailto:owner-amber.scripps.edu] On Behalf Of Pradipta Bandyopadhyay
>> Sent: Monday, May 15, 2006 6:53 AM
>> To: amber.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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>
Dr. Pradipta Bandyopadhyay
Assistant Professor
Dept. of Biotechnology
Indian Institute of Technology, Guwahati
Phone: 91-361-258-2213 (office)
e-mail: pradipta.iitg.ernet.in
web: http://202.141.80.5/~pradipta/Pradipta.htm
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Received on Wed May 17 2006 - 06:07:13 PDT
