On Thu, Sep 1, 2011 at 11:36 PM, Ismail, Mohd F. <farid.ou.edu> wrote:
> Thanks Jason. I understand what you mean. I'm trying to solvate ions,
> where the anion is not a simple ion. But the cation is Li+.
>
> So I have to load the prep.in for the anion, and then do addions unit li+
> 0 before I can solvate the whole ion. So the method you mentioned would
> have worked if I can either saveamberprep for the anion + cation (I've tried
> to saveamberprep the anion + the cation, but leap just segfault and crashed;
> creating a prep.in for a single monoatomic cation will error out with leap
> with illegal entry message), or if I can saveamberparm and edit the prmtop
> and inpcrd after I edited the pdb file. I looked inside the inpcrd but I'm
> not sure quite sure about the format. A short search on google didn't
> produce anything clear enough to me.
>
The inpcrd file is fairly straightforward. It is described here in detail
http://ambermd.org/formats.html#restart. I don't think I understand what
you're trying to do or why you're trying to do it. If the anion isn't in
Amber's standard residue libraries, you'll need to create your own library
file (using antechamber or R.E.D. or something of the sort). You can use a
mol2 file, Amber prep file, or OFF file for this (I would suggest mol2,
especially for an isolated ion without any connectivity information). You
do not need leap to create this file (I would suggest *not* using leap).
>
> One method that I've tried that worked is to load the prep for the anion
> plus the solvent, then do addions unit li+ 0, but li+ added are outside the
> box, that I have to set the initial box size quite big or minimization won't
> go pass a few steps before linmin failure occurs. When I set the box size
> to very big, the file produced will have a very low density. I have tried
> to equilibrate the box back to appropriate density and so far it is a very
> slow process. I will try with higher pressure to make it faster.
>
linmin failures are not that bad -- see their description here:
http://ambermd.org/Questions/linmin.html. If you followed my advice, you
should be able to figure out what a reasonable box size should be for your
system just by looking at the original box size for the system when you
first created the PDB to remove waters from. Then make sure you equilibrate
density. If your box is way too big, it will take too long to relax your
density to a reasonable value.
>
> I'm just looking for easier ways to do this. Is there a way to create
> prep.in for li+ or any monoatomic cation?
>
I don't see why you have to create the prep.in in the first place. The Li+
parameters are in Amber's standard residue library (you have to load a
solvent-specific frcmod file for ions in FF10). I have rarely (if ever)
found that I *needed* to use saveamberprep in leap. It doesn't seem to have
much use to me -- if you already have the library file (in MOL2 or Amber OFF
format), why would you need to print out another one in a rarely-used
format?
Hopefully this was helpful,
Jason
> I appreciate any input.
>
> --Farid
>
> ________________________________________
> From: Jason Swails [jason.swails.gmail.com]
> Sent: Thursday, September 01, 2011 8:54 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] solvateBox
>
> On Thu, Sep 1, 2011 at 9:49 PM, Jason Swails <jason.swails.gmail.com>
> wrote:
>
> > molecules you want, but make sure that you have a few too many (rather
> than
> > too few).
> >
>
> I realize this may be confusing wording. Make sure that if you want 100
> water molecules, you have at least 100 (101, 102, etc.). You don't want
> too
> few (i.e. 99, 98, etc.).
>
>
> >
> > Then load that PDB back into leap (with the correct number of waters),
> and
> > use the "setbox" command (find it in the AmberTools manual for how to use
> > it) to apply periodic boundary conditions.
> >
> > HTH,
> > Jason
> >
> >
> >> --Farid
> >> _______________________________________________
> >> AMBER mailing list
> >> AMBER.ambermd.org
> >> http://lists.ambermd.org/mailman/listinfo/amber
> >>
> >
> >
> >
> > --
> > Jason M. Swails
> > Quantum Theory Project,
> > University of Florida
> > Ph.D. Candidate
> > 352-392-4032
> >
>
>
>
> --
> Jason M. Swails
> Quantum Theory Project,
> University of Florida
> Ph.D. Candidate
> 352-392-4032
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
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> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
--
Jason M. Swails
Quantum Theory Project,
University of Florida
Ph.D. Candidate
352-392-4032
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Received on Thu Sep 01 2011 - 21:00:03 PDT
