The old style impropers should be fine. I don't see obvious problems
with the structure either.
I'm running your simulation now in an attempt to reproduce the
situation. Will get back to you.
On Mon, Feb 20, 2012 at 9:54 AM, <tommaso.casalini.mail.polimi.it> wrote:
> 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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--
:-) Lachele
Lachele Foley
CCRC/UGA
Athens, GA USA
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Received on Mon Feb 20 2012 - 08:30:02 PST
