On Oct 18, 2010, at 11:19 AM, balaji nagarajan wrote:
>
> Dear amber !
>
> I have solvated a peptide with the solvent using packmol
> the solvent (organic ) is not in the amber library .
>
> I have enclosed the peptide in the solvent sphere .
>
> Now I tried minimising the system with ntb=1 ,
>
> but the minimization stopped , when i gave the ntb=0 , the minimization was done .
>
> This is also the same problem like the solvateshell ? as i earlier asked or else it is possible to fix the
> periodic boundary for a sphere ?
>
> I would like to know the interaction between the solvent and the
> solute is it possible to do in amber ?
>
>
> thanks in advance
>
I was just about to post an email about things to watch out for when using packmol
to generate AMBER input. I have not finished some simulations for which I want
results before I post the email, but as a suggestion do something like this:
Generate a cube of solvent around your peptide so that you can use PBC later on.
Solvent spheres have a unique set of problems that are bypassed if you use a
simulations with PBC.
As an example:
I generated a 500 molecule cube, 24.83535125 A on a side, of TIP3P waters (the cube
side was calculated to give the same number density as the 216 molecule water boxes
used by LEaP to solvate systems).
Generate a coordinate and topology file with box information:
tleap -f tleap.script
where tleap script is:
source leaprc.ff99SB
X = loadpdb water_cube.pdb
set X box 24.83535125
saveamberparm X water_cube.prmtop water_cube.inpcrd
quit
You will of course use your solvent cube pdb file and its dimensions, not
water_cube.pdb and 24.83535125, and you should name the output files
appropriately.
Then minimize the system (substitute the names of your topology and coord
files):
sander -p water_cube.prmtop -c water_cube.inpcrd
where your mdin is similar to:
Minimization with NO Cartesian restraints
&cntrl
imin=1, maxcyc=500,
ntpr=5,
ntr=0,
/
You may want Cartesian restraints on your solute. This mdin is derived from
the example at the front of the AMBER documentation (and that example does
use Cartesian restraints). Assuming that the energy drops to a reasonable
value, carry out NPT molecular dynamics for a fairly extended duration.
With the water cube, the VDWAALS was extremely large for the initial frames
of the minimization, but the total energy had turned negative by the 40th
frame. I would use something like 5ns NPT MD for small solutes, but
whatever duration you use search the email list for postings outlining
criteria for successful equilibration.
Hope this helps.
Bud Dodson
--
M. L. Dodson
Business email: activesitedynamics-at-comcast-dot-net
Personal email: mldodson-at-comcast-dot-net
Phone: eight_three_two-five_63-386_one
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Received on Mon Oct 18 2010 - 10:30:04 PDT
