Re: amber-developers: experience with sleap

From: David A. Case <case.scripps.edu>
Date: Tue, 17 Apr 2007 10:18:13 -0700

On Tue, Apr 17, 2007, Wei Zhang wrote:

> There is such a option to echo input command in sleap, by default it is
> turned off, you can turn it on by typing:
>
> set default echo on

I think this should be the default, with an option to turn it off. Note that
sleap is not completely quiet anyway, so having this default to "on" seems to
make good sense to me.

> I can make sleap to accept "-f" option.

thanks.
>
>
> >5. The dihedral angle energy is different for tleap and sleap, even when
> >all atoms are present in the input pdb file. My guess is that some improper
> >dihedral term has a different order of atoms, but I'm not sure of that. I'll
> >have to create a debug version to print out all the dihedrals to track this
> >down.
> >
> >
> Yes, mostly likely it is because of the improper dihedral. Can you also send
> me a copy of you pdb file?

The pdb file is attached. Here is the tleap script I used:

source leaprc.ff99SB
x = loadPdb 1ubq.reduceH.pdb
saveamberparm x prmtop.tleap eq0.tleap.x
quit

And here is the sleap script:

source leaprc.ff99SB
x = loadPdb 1ubq.reduceH.pdb
saveamberparm x prmtop.sleap eq0.sleap.x
quit


>
> >Also, NEXT, NUMBND, NUMANG and NATYP are different in the sleap prmtop than
> >in the tleap prmtop: are these expected differences?
> >
> >
> I will look into this right now, should be easy to fix it.

Great....regards...dave




Received on Wed Apr 18 2007 - 06:07:36 PDT
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