Hi,
Amoeba is a totally different force field from AMBER. They have
different function form.
so yes AMOEBA is not compatible with gaff.
Sincerely,
Wei
On Mon, Sep 5, 2011 at 7:10 AM, Guenegou, Guillaume [JRDFR] <
GGUENEGO.its.jnj.com> wrote:
> Dear all,
>
>
>
> I work with amber 11 and ambertools 1.5 (patched).
>
>
>
> I am trying to use leaprc.amoeba in sleap.
>
> Here is my input file :
>
>
>
> source leaprc.amoeba
>
> source leaprc.gaff
>
>
>
> frcmod1 = loadamberparams 1.frcmod
>
>
>
> prot = loadpdb protein.pdb
>
> lig = loadmol2 ligand.mol2
>
>
>
> complex = combine {prot lig}
>
> saveamoebaparm complex complex.top complex.crd
>
>
>
> quit
>
>
>
>
>
>
>
> This works fine with leaprc.ff03.r1 or others. But using leaprc.amoeba,
> I get the following message when sleap try "saveamoebaparm ...":
>
> "get typeid of -1
>
> Error (get_iptr): while retrieving parameter typeid, impossible abs ID
> (-1)"
>
>
>
> Is it because gaff and amoeba are not compatible?
>
>
>
>
>
> G.GUENEGOU
>
>
>
>
>
> PS : cannot have access to amber mailing list archives, so I could not
> check if there is a solution already posted...
>
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> AMBER mailing list
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> http://lists.ambermd.org/mailman/listinfo/amber
>
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Received on Mon Sep 05 2011 - 14:30:05 PDT
