Re: [AMBER-Developers] sleap issues

From: Lachele Foley <lfoley.ccrc.uga.edu>
Date: Thu, 10 Dec 2009 11:32:43 -0500

It built the molecule this time, but some of the sleap-generated atom positions seem wonky. The two programs also generate different default inter-residue torsions. I've attached top and crd from both builds. The files that start with "s" were built using sleap. I'm using the same input files I sent before.

The easiest place to see the "wonky" atom positions is to look at the "NAc" part (NH-CO-CH3) of the two GlcpNAc residues, but there are others. I viewed them by opening the top and crd files in vmd. A minimization would probably fix the atom position issues, which don't seem severe at this cursory-glance level, but the build should look better at the start.

Regarding the torsions, for example, the LeAP input file specifies:

impose glycan {3 2} { {C1 O4 C4 H4 0.0} } # set psi between 4YB & 4YB

VMD measures:

tleap: Info) Added new Dihedrals label 4YB2:H4/4YB2:C4/4YB2:O4/4YB3:C1 = 0.000014

sleap: Info) Added new Dihedrals label 4YB2:H4/4YB2:C4/4YB2:O4/4YB3:C1 = -61.545046


:-) Lachele

--
B. Lachele Foley, PhD '92,'02
Assistant Research Scientist
Complex Carbohydrate Research Center, UGA
706-542-0263
lfoley.ccrc.uga.edu
----- Original Message -----
From: Wei Zhang
[mailto:zgjzweig.gmail.com]
To: AMBER Developers Mailing List
[mailto:amber-developers.ambermd.org]
Sent: Wed, 09 Dec 2009 23:18:49
-0500
Subject: Re: [AMBER-Developers] sleap issues
> Hi Lachele,
> 
>     I just checked in a bugfix which should resolve the second problem you
> have encountered.
> e.g. "sparm type does not exist".  Would you please check it out and give
> sleap another try?
> 
>     I will need some more time to implement the in-line comment thing.
> 
>     Thank you very much!
> 
>     Sincerely,
> 
>     Wei
> 
> 
> On Dec 9, 2009, at 3:53 PM, Lachele Foley wrote:
> 
> > I'm trying to make sure the AmberTools documentation examples work for
> sleap this time around and found these.  Sorry I didn't find them before...
> > 
> > 1] sleap doesn't allow in-line comments like tleap does.  I love to
> comment my code, especially when sharing.  It would be great if it were
> possible to do that though I admit this isn't critical.  If not made
> consistent with tleap, the difference should at least be documented.  For
> example, in tleap I can successfully do something like:
> > 
> > impose glycan {3 2} { {C1 O4 C4 H4 0.0} }       # set psi between 4YB &
> 4YB
> > 
> > ...but in sleap, this happens:
> > 
> > [gtkleap]$ impose glycan {3 2} { {C1 O4 C4 H4 0.0} } # set psi between 4YB
> & 4YB
> > Error: wrong number of arguments 
> > 
> > 
> > 2] tleap happily builds me a topology and coordinate set from the attached
> input (see also the output), but sleap gives the following:
> > 
> > [gtkleap]$ saveamberparm glycan glycan.top glycan.crd  
> > Error: sparm type does not exist!
> > 
> > 
> > 3] I have no clue what that last error message means (sleap doesn't know
> the parm type?).  I checked the manual and the term 'sparm' doesn't appear. 
> The programmer's guide mentions 'sparm', but only in the context of a
> declaration.  I realize it might be a tough order to fill, but either making
> the error messages more descriptive or documenting them well would be very
> useful.
> > 
> > 
> > :-) Lachele
> > --
> > B. Lachele Foley, PhD '92,'02
> > Assistant Research Scientist
> > Complex Carbohydrate Research Center, UGA
> > 706-542-0263
> >
> lfoley.ccrc.uga.edu<linear.leapin><linear.sleapin><tleap.out><sleap.out>_______________________________________________
> > AMBER-Developers mailing list
> > AMBER-Developers.ambermd.org
> > http://lists.ambermd.org/mailman/listinfo/amber-developers
> 
> 
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> 

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Received on Thu Dec 10 2009 - 09:00:02 PST