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.
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.
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 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
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Received on Thu Sep 01 2011 - 21:00:02 PDT
