Hi all,
I tried both with tleap and sleap (AmberTools 1.4) and nothing changes.
I performed a quick simulation in implicit solvent and the hydrogen
issues still remain.
I observed the structure that leap gives to me, but I was not able to
find the incorrectly placed hydrogens.
Moreover, tleap tells me that it must apply some old-prep improper
torsions, while sleap does not.
Thank you for your help.
Tommaso Casalini, Ph.D fellow
CFA lab, Politecnico di Milano
Def. Quota David A Case <case.biomaps.rutgers.edu>:
> On Sat, Feb 18, 2012, Karl N. Kirschner wrote:
>>
>> I have encountered a similar problem recently, I don't think it
>> involves the glycam06g force field directly, but something with how
>> xleap (didn't try tleap) interprets the force field when sourcing the
>> protein/dna force field. If you look at the output structure of leap,
>> I think you will see that a few of the hydrogen atoms are incorrectly
>> placed. I corrected this by only loading glycam06 parameters and
>> suppressing the the protein force field loading (i.e. xleap -s -f
>> leap.in). This then gave me the correct spatial structure of the
>> carbohydrate.
>
> Hi Karl:
>
> Thanks for the info. Can you post a specific example? We need to track this
> down. If LEaP is actually adding hydrogens in incorrect ways, it should be
> fixed. (I doubt that there is any difference between tleap and xleap, since
> most of their code is shared.)
>
> Are there other codes that are more reliable in adding hydrogens to
> carbohydrates? "Reduce" does a good job for proteins, but I
> doubt(?) that any
> third-party program would know about all the atom and residue names used by
> GLYCAM. Either you or someone else might check sleap, since it would be
> helpful to know if the latter worked better than tleap/xleap.
>
> ...thanks!...dave
>
> (cc-ing to amber-developers as well)
>
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>
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Received on Mon Feb 20 2012 - 07:00:03 PST
