AMBER Archive (2009)

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

From: Alan (alanwilter_at_gmail.com)
Date: Tue Dec 29 2009 - 15:47:52 CST

Hi Watson,

This is indeed a great tip.

For the problem I reported with sleap, I am sure am running AT 1.3 with the
proper setup.

Thanks!

Alan

On Tue, Dec 29, 2009 at 21:02, David Watson <dewatson_at_olemiss.edu> wrote:

> 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 voilà, 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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> AMBER_at_ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
> 

-- 
Alan Wilter Sousa da Silva, D.Sc.
PDBe group, PiMS project http://www.pims-lims.org/
EMBL - EBI, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
+44 (0)1223 492 583 (office)
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