On Jul 23, 2013, at 2:45 PM, M. L. Dodson wrote:
>
> On Jul 23, 2013, at 2:19 PM, Chinthaka Ratnaweera wrote:
>
>> I followed the procedure in tutorial 15.
>>
>> This is my packmol input file
>>
>> tolerance 2.0
>> output ethbox.pdb
>> filetype pdb
>> structure ethanol.pdb
>> number 1000 # Number of molecules
>> inside cube 0. 0. 0. 50. # x, y, z coordinates of box, and length of box in
>> Angstroms
>> end structure
>>
>> Then use leap to generate initial coordinates and topologies.
>> source leaprc.gaff
>> ETH = loadmol2 ethanol.mol2
>> ETHBOX = loadpdb ethbox.pdb
>> setbox ETHBOX centers
>> saveAmberParm ETHBOX ethbox.prmtop ethbox.inpcrd
>>
>> But when running minimization under NVT it gave me this error
>> forrtl: severe (174): SIGSEGV, segmentation fault occurred
>>
>> my minimization input is
>> test run 1
>> &cntrl
>> imin = 1, ntpr = 100, ntwx=100, maxcyc = 10000, ntb=1
>> &end
>>
>> This starts the first step of minimization
>> TESTING RELATIVE ERROR over r ranging from 0.0 to cutoff
>> | CHECK switch(x): max rel err = 0.2738E-14 at 2.422500
>> | CHECK d/dx switch(x): max rel err = 0.8314E-11 at 2.736960
>> ---------------------------------------------------
>> | Local SIZE OF NONBOND LIST = 1264139
>> | TOTAL SIZE OF NONBOND LIST = 1264139
>>
>>
>> NSTEP ENERGY RMS GMAX NAME NUMBER
>> 1 2.1423E+09 4.7538E+08 4.7855E+10 H4 2698
>>
>> BOND = 547891.8779 ANGLE = 201752.1037 DIHED =
>> 2455.8141
>> VDWAALS = ************* EEL = 12317.8836 HBOND =
>> 0.0000
>> 1-4 VDW = 72044523.0714 1-4 EEL = -22796.8084 RESTRAINT =
>> 0.0000
>>
>>
>> Is this because of my box size?
>>
>>
>
> Probably not. Boxes created with packmol are not equilibrated with periodic boundaries.
> Packmol just puts packs spheres (connected spheres in the case of ethanol.) At the
> box boundaries, parts of molecules extend beyond the box. When the boxes are tiled,
> some of the atoms overlap with the next image so you get VDW clashes. You need a box
> bigger than the packmol box when you tile the boxes, then equilibrate at constant
> pressure to shrink the box, equilibrate the density, and arrange the box edges to be
> consistent with periodic boundaries.
>
Let me make this less ambiguous.
Your Packmol box is not the problem, the box assigned by LEaP is too small if it is
the same as the Packmol box. Boxes created with packmol are not equilibrated with
periodic boundaries. Packmol just puts packs spheres (connected spheres in the case
of ethanol.) At the Packmol box boundaries, parts of molecules extend beyond the box.
When the boxes are tiled with LEaP, some of the atoms overlap with the next image so
you get VDW clashes. You need a LEaP box bigger than the packmol box when you tile
the boxes, then equilibrate at constant pressure to shrink the PBC box, equilibrate
the density, and arrange the PBC box edges to be consistent with periodic boundaries.
> Good luck,
> Bud Dodson
>
>> On Tue, Jul 23, 2013 at 10:02 AM, David A. Case <case.biomaps.rutgers.edu>wrote:
>>
>>> On Mon, Jul 22, 2013, Chinthaka Ratnaweera wrote:
>>>>
>>>> Once the saveoff command make a box 'unit' ( I guess I have to save it
>>> as
>>>> a lib file), inorder to use that unit to solvate the protein, do I have
>>> to
>>>> use loadoff command to open it and give this unit name as second argument
>>>> in solvatebox command?
>>>
>>> Yes.
>>>
>>>>
>>>> Does size of the solvate box matters when setup the initial box using
>>>> packmol?
>>>
>>> It's not a big deal which size you choose. Most of the "standard" boxes
>>> are really smaller than they should be (some were made back in the 1980s
>>> when
>>> computers were much slower.) The solvateBox and solvateOct routines will
>>> replicate and truncate boxes as needed. Something on the order of 1000
>>> ethanol molecules should be fine.
>>>
>>> ...good luck....dac
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>
>>
>>
>> --
>> Chinthaka Nadun Ratnaweera
>> Hand Lab Rm 1126
>> Mississippi State University
>> 310 Presidents Circle
>> Starkville, MS 39762
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
> --
> M. L. Dodson
> Business email: activesitedynamics-at-gmail-dot-com
> Personal email: mldodson-at-comcast-dot-net
> Gmail: mlesterdodson-at-gmail-dot-com
> Phone: eight_three_two-five_63-386_one
>
>
>
>
>
>
>
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--
M. L. Dodson
Business email: activesitedynamics-at-gmail-dot-com
Personal email: mldodson-at-comcast-dot-net
Gmail: mlesterdodson-at-gmail-dot-com
Phone: eight_three_two-five_63-386_one
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Received on Tue Jul 23 2013 - 13:00:03 PDT
