Thanks Jason. That's true. I wasn't thinking.
I know gaff doesn't have Li+ parameters. I will try ff03.
--Farid
________________________________________
From: Jason Swails [jason.swails.gmail.com]
Sent: Friday, September 02, 2011 12:42 AM
To: AMBER Mailing List
Subject: Re: [AMBER] solvateBox
On Fri, Sep 2, 2011 at 12:02 AM, Ismail, Mohd F. <farid.ou.edu> wrote:
> So, if I read in coordinates for Li+ in my pdb file, I don't have to read
> in the parameter for it? I can just source appropriate leaprc file? I
> didn't think of that. So far I have been doing:
>
> loadamberprep anion.prep
> loadamberparams anion.frcmod
> anion = loadpdb anion100.pdb
> loadamberprep mysolvent.prep
> loadamberparams mysolvent.frcmod
> mysolvent = loadpdb solvent100.pdb
> then I do addions .....
>
> So, if I just source, says leaprc.ff99, I can just do
> li = loadpdb li100.pdb ?
>
> My system is organic solvent with ions in them. Much like electrolytes
> system. I have created the charges for my anion from mol2 using RED. The
> parameters are gaff's.
> I'm not near my machine, but I will try that tomorrow.
>
You don't have to load prep/mol2/OFF files for any residue that is in
Amber's standard residue library (namely all of the standard amino acids,
nucleic acids, monatomic ions, TIPnP waters). Anything that's not in that
library you have to load one for (like a prep file).
Also, I would suggest against using leaprc.ff99, since it's a very old force
field with known problems, especially for proteins.
HTH,
Jason
>
> Thank you for all ideas.
>
> --Farid
> ________________________________________
> From: Jason Swails [jason.swails.gmail.com]
> Sent: Thursday, September 01, 2011 10:51 PM
> To: AMBER Mailing List
> Subject: Re: [AMBER] solvateBox
>
> 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
> >
> > _______________________________________________
> > 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
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
> _______________________________________________
> 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
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Received on Fri Sep 02 2011 - 09:30:03 PDT
