Following up on my own email, I meant this happened during the minimization run
when I said:
> 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.
Bud Dodson
On Oct 18, 2010, at 12:07 PM, M. L. Dodson wrote:
>
> 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
>
>
>
>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
--
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
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Mon Oct 18 2010 - 10:30:05 PDT
