Hello,
I made a water box from this command
=================================
AddToBox -c 20.pdb -a water.pdb -na 2500 -o 20wat.pdb -P 800 -RP 0.75
-RW 1.4 -V 1 -X 52.22 -Y 46.34 -Z 40 -al 90 -bt 90 -gm 120
===================================
And I store only waters to 20wat.pdb file again.
After loading all files in leap, I was able to generate prmtop and
inpcrd file.
=======================================
source leaprc.ff99SB
source leaprc.gaff
loadamberprep c2.prepi
loadamberparams c2.frcmod
gr=loadpdb 20.pdb
bondByDistance gr 1.5
savepdb gr 20amb.pdb
ww=loadpdb 20wat.pdb
grw= combine {gr ww}
setbox grw vdw 1.0
saveamberparm grw c20w.prmtop c20w.inpcrd
=======================================
Next, I changed BOX information in prmtop file to shrink the x
dimension and changed the box information(the last row) in inpcrd file
according to prmtop file and change all angles to 90 90 120.
And It passed the minimization MD.
Thank you.
Bongkeun Kim
Quoting dcerutti.rci.rutgers.edu:
> This might be a good use of the "AddToBox" utility; you can download it from
>
> http://ambermd.org/tutorials/advanced/tutorial13/XtalTutor1.html
>
> (it's the first link, hiding in the second paragraph). That archive
> contains a lot of different things, but if you follow
>
> http://ambermd.org/tutorials/advanced/tutorial13/Solvation.html
>
> you should be able to run AddToBox to insert whatever number of waters you
> want. They won't be in any equilibrated conformations, but I'd argue that
> no equilibration matters if you're tiling the pre-equilibrated box around
> some arbitrary solute and then clipping away waters that clash.
>
> AddToBox can handle any unit cell shape; it takes PDB files of your solute
> and a model of your solvent particle as input and returns a PDB file of
> the whole system.
>
> Dave
>
>> Hello,
>>
>> I want to solvate a graphite surface according to its shape.
>> Because angles are 90, 90, 120, the simple solvaetbox command in leap
>> ----------------------------------------------------------
>> source leaprc.ff99SB
>> source leaprc.gaff
>> loadamberprep c2.prepi
>> loadamberparams c2.frcmod
>> gr=loadpdb 40.pdb
>> bondByDistance gr 1.5
>> savepdb gr 40amb.pdb
>> solvatebox gr TIP3PBOX {0 0 20}
>> saveamberparm gr c40.prmtop c40.inpcrd
>> --------------------------------------------
>> can make the extra water space along in the xy plan(see the image file).
>> Do you think it is possible to make a triclinic PBC box instead of the
>> cubic box from leap?
>> Thank you.
>> Bongkeun Kim
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
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>
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Received on Fri Oct 22 2010 - 12:30:03 PDT
