Hi Lachele,
Thank you for your reply! I am working on it now.
Sincerely,
Wei
On Dec 10, 2009, at 10:32 AM, Lachele Foley wrote:
> 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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Received on Thu Dec 10 2009 - 14:00:04 PST
