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?
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
>
>
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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
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Received on Tue Jul 23 2013 - 12:30:02 PDT
