AMBER Archive (2009)

Subject: Re: [AMBER] Fail to allocate ff

From: Gustavo Seabra (gustavo.seabra_at_gmail.com)
Date: Tue Mar 03 2009 - 14:36:53 CST

On Tue, Mar 3, 2009 at 6:17 AM, Madhurima Jana <tinni.217_at_gmail.com> wrote:
> Hi All,
>
> I want to perform a MD simulation of CCL4 box using AMBER force field.
> For that I want to create the corresponding inpcrd and parmtop files.
> Actually my system contains 900 CCL4 molecule in an orthorhombic box.
> Using antechamber I was able to create a mol2 file for a single CCL4
> molecule and from that the corresponding  inpcrd and parmtop files.
> But whenever I'm trying to do so for 900 molecules [...]

If I understood correctly what you want to do, there's no reason for
you to create such a huge thing with antechamber. Actually, there's no
reason to even expect that would work: Antechamber was not created to
deal with very large systems. Besides, what you probably want is a
system built of CCl4 units, not a big superunit composed of many CCl4
units, is it?

Once you have the parameters for CCl4, load them into LEaP, than build
your system with something like:

    [assuming you have already loaded the CCl4 molecule in LEaP, and
it shows up as a unit if you try 'list']

    mol1 = ccl4
    solvatebox mol1 ccl4 12.0

this should create a box with enough CCl4 molecules around the
original one for a 12.0 angstroms buffer. You can play with the buffer
size to get the number of molecules you want.

HTH,
Gustavo.

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