On May 7, 2014, at 2:13 AM, Mari Mak <mmakrides1.gmail.com> wrote:
> To whom it may concern,
>
> Hello, I am learning Amber for the first time, and I would really
> appreciate any advice/tips you can offer.
>
> I would like to build a box of 1-octanol molecules and use the GAFF force
> field to perform MD simulations. I have gone through several of the
> tutorials available online (enormously helpful, by the way) and had success
> running MD on a single molecule of 1-octanol.
>
> I have built pdb files for boxes of octanol molecules using other programs,
> but I was unable to get Amber to read these files properly. Can Xleap, or
> any of the other utilities within Amber, be used to build a pdb file
> corresponding to a box of several (e.g., a few hundred) octanol molecules?
> Thank you for your time.
Yes, this can be done. In fact, if you have already simulated a single octanol molecule, then you already have most of the files you need to do this. The first thing you need to do is to create a PDB file with a box of octanol molecules (this is by far the hardest part of everything you have left to do).
While you _can_ have Amber do this (by a series of "copy" and "translate" commands in tleap), I would suggest using another tool that is optimized for this purpose. A good example is packmol, which can be used to create a box of octanol molecules and spit back a PDB file.
Once you have this PDB file, it is important that the atom names and residue name matches exactly the mol2 file you got from antechamber (I assume you got a mol2 -- it could also be an Amber prep, although mol2 is a better format IMO). Then all you have to do is load your mol2 file as the residue name as well as the gaff force field and any frcmod file you had to generate (using parmchk, for instance). So your tleap script would look something like this (assuming packmol gave you a PDB file "box_of_octanol.pdb"):
source leaprc.gaff
OCT = loadMol2 octanol.mol2
loadAmberParams octanol.frcmod
octbox = loadPDB box_of_octanol.pdb
setBox octbox centers
saveAmberParm octbox octbox.parm7 octbox.rst7
The above script assumes you created an octanol.mol2 file and that the octanol residue name is OCT (change that to whatever is appropriate for you).
The point is that you already got tleap to recognize the octanol residue in a PDB with a single octanol when you simulated a single octanol (the hard part!). That means it will recognize that residue no matter how many times it appears in a PDB file.
Hope this helps,
Jason
--
Jason M. Swails
BioMaPS,
Rutgers University
Postdoctoral Researcher
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Received on Wed May 07 2014 - 05:00:05 PDT
