AMBER Archive (2009)

Subject: Re: [AMBER] sleap in AmberTools 1.3 is not working anymore for me

From: David Watson (dewatson_at_olemiss.edu)
Date: Tue Dec 29 2009 - 15:02:05 CST

On Dec 29, 2009, at 2:27 PM, Alan wrote:

> Dear all,
>
>
> This used to work pretty fine with AT 1.2, without any warning, but now with
> AT 1.3 ...:
>
> - Extract ligand DMP from 1BVG, name it Ligand.pdb
>
> - Enter sleap terminal command and enter:
> [gtkleap]$ source leaprc.ff99SB
> [gtkleap]$ source leaprc.gaff
> Info: ignoring unknown atom type: h
> Info: while reading ANGL. Input: f c h 51.5 109.90 SOURCE2
> 1 0.0000 0.0000
> Info: ignoring unknown atom type: h
> Info: while reading ANGL. Input: h c o 53.1 127.30 SOURCE2
> 1 0.0000 0.0000
> Info: ignoring unknown atom type: cb
> Info: while reading DIHE. Input: X c1 cb X 2 0.000 180.000
> 2.000
> Info: ignoring unknown atom type: cb
> Info: while reading DIHE. Input: X n1 cb X 2 0.000 180.000
> 2.000
> # { why these info above ?}
>
> [gtkleap]$ set default fastbld on
> [gtkleap]$ DMP = loadpdb Ligand.pdb
> Warning: cannot find template for residue DMP in our library.
> You will not be able to save prmtop for this molecule.
> [gtkleap]$ saveamberparm DMP Ligand_AC.prmtop Ligand_AC.inpcrd
> Error: dparm pchg does not exist!
>
>
> I am using a AT 1.3 compiled with intel on Mac OSX 10.6.2 64 bits.
>
> Many thanks in advance,
>
> Alan

One thing that you may want to check is whether or not you have set AMBERHOME=/path/to/amber11, and also make sure that you prepend AMBEROME/bin to your path (i.e. "export PATH=/path/to/amber11/bin:$PATH") before you try this run.

You may want to create a bash function to do this for you when you plan on using AT1.3:

#add this to ~/.bash_profile
function useAT13() {
    export AMBERHOME=/path/to/amber11
    export PATH=$AMBERHOME/bin:$PATH
}
# end of additions

Then, when you have started a new Terminal session, assuming you would like to use AT1.3, type:
    useAT13
and voilą, everything should be set right.
You might want to do it this way in order to preserve the functionality of Amber9 or Amber10, due to the change in paths.

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