AMBER Archive (2005)

Subject: Re: AMBER: mm_pbsa problem

From: Scott Pendley (scott.pendley_at_gmail.com)
Date: Tue Nov 01 2005 - 16:36:48 CST

Check your mm_pbsa input script. I have received a similiar error when I
have told to it run without providing snapshot crd files or told it to
generate snapshot crd files.

On 11/1/05, Cenk Andac <cenk_andac_at_yahoo.com> wrote:
>
> Hello,
>
> > =>> Treat special parameters
> > =>> Calc missing parameters
> > =>> Calc delta from raw data
>
> It seems to me that you have an unusual residue that
> is not defined in AMBER force field. In that case, I
> would suggest that you prepare your parameter-topology
> and coordinates files using General AMBER Force Field
> which can be called in by typing 'source leaprc.gaff'
> in leap.
> In that case, I would also recommend that you prepare
> a mol2 file for your molecule by antechamber using
> GAFF atom types and AM1BCC charges. You could then use
> that mol2 file as an input in leap to prepare your
> prm/top and crd files.
>
> That is all I can propose to help solve your proplem
> looking at your mm-pbsa output. Perhaps, someoneelse
> can come up with a better solution.
>
> wishing you a plenty of luck with your reserach.
>
> jenk.
>
>
>
>
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