On Jul 23, 2013, at 3:10 PM, Chinthaka Ratnaweera wrote:
> Ok
> I used 'setbox ETHBOX vdw {5,5,5}'
> It make a box bigger than previous.
>
> The box dimensions now read as
>> setbox ETHBOX vdw {5,5,5}
> Box dimensions: 65.435279 64.286901 64.791138
>
> my Packmol box should be 50*50*50. Is this size enough now?
>
> but this gives the same problem in minimization. Are you mean I have to do
> the equilibration at constant pressure without minimization? I try that
>
I've been away from this stuff for a couple of years, so all I can comment is
that the boxes set with LEaP and Packmol were not oriented the same (if I
remember correctly.) I figured this out a couple of years ago, but the details
are hazy. IIRC, the most foolproof way I found was to create (counter
intuitively) an origin-centered sphere with the correct number of molecules.
Then enclose the sphere with with a truncated octahedron substantially bigger
than the sphere. If your packmol structure is not tightly packed, you can
probably get away with no (or minimal) minimization. Of course the larger
the truncated octahedron "box," the longer the constant pressure run to
equilibrate the density.
I MAY have had to make sure the trunc. oct. and the sphere were co-centered,
I can't remember.
After you get an equilibrated restart file, you can cut out an appropriately
sized cube with ptraj (IIRC, although can't remember the exact commands.)
Good luck,
Bud Dodson
PS, another way to do this is to use a PDB with only a single molecule, then
"solvate" that molecule with more of the same molecule. This is probably
less trouble than using Packmol for single species boxes. Packmol is needed
for mixtures, though, I believe.
> On Tue, Jul 23, 2013 at 2:52 PM, M. L. Dodson <mldodson.comcast.net> wrote:
>
>>
>> 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
>>>> _______________________________________________
>>>> AMBER mailing list
>>>> AMBER.ambermd.org
>>>> 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
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> 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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>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> Chinthaka Nadun Ratnaweera
> Hand Lab Rm 1126
> Mississippi State University
> 310 Presidents Circle
> Starkville, MS 39762
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> 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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Received on Tue Jul 23 2013 - 13:30:03 PDT
