On Jul 2, 2013, at 9:34 AM, Brian Radak <radak004.umn.edu> wrote:
> Thanks for the quick replies.
>
> On closer inspection it would appear that all hydrogens are getting typed
> correctly (*i.e.* the specific type is indicative of the connectivity), but
> hydrogens bound to carbon all get the "HC"-type LJ parameters (hydrogens
> bound to nitrogen are just fine). I don't have much interest in figuring
> out what is going on in PARMCHK.DAT in order to fix this (does anybody know
> what the tables in there mean?).
>
> Fortunately parmed should let me just correct the LJ parameters based on a
> type selection. Unfortunately, I'm not sure the ".%" ambmask syntax is
> working properly in the Python implementation at the moment and Jason is
> out of the office for the week.
It should be working properly. I've used it many times in the past (and it is very similar code to just . except the atom type names are searched instead). If you tell me what you are inputting and what you are expecting, I may be able to help here.
Have you compared the python mask selection and the one from cpptraj and ambmask, too?
>
> I guess I can just do this by hand in tleap.
>
> Brian
>
>
> On Tue, Jul 2, 2013 at 3:45 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>
>> Dear Brian,
>>
>> There is no difficulty for differentiating the 'HC' atom type vs the
>> 'H1', 'H2' or 'H3' ones; i.e. is a given hydrogen atom, which is
>> connected to a carbon atom connected to one, two or three heteroatoms.
>> The same rule applies for the aromatic hydrogens 'HA', vs 'H4' and
>> 'H5'... These 'HC' vs 'H1'/'H2'/'H3' and 'HA' vs 'H4'/'H5' definitions
>> are at the basis of the Cornell et al. force field; and there is no
>> difficulty for coding that...
>>
>> R.E.D. Python fully handles this quite basic problem (differentiating
>> the different double bonds is far more complex for instance); I invite
>> you to use R.E.D. Python when available i.e. sometimes next
>> September/October 2013.
>> You can also use R.E.D. Server and request a private assistance to
>> post-process your data with R.E.D. Python.
>>
>> regards, Francois
>>
>>
>>> I'm running calculations on a bunch of nucleic acids and analogues. Since
>>> these are non-standard non-nucleobase compounds I used antechamber to
>>> assign atom types. However, it would appear that the hydrogen
>> Lennard-Jones
>>> parameters for atoms of the same type do not match in prmtops generated
>>> from antechamber files and those from leaprc.ff10
>>>
>>> (using parmed.py printDetails)
>>> Rmin/2 epsilon
>>> type AC FF10 AC FF10
>>> H4 1.4870 1.4090 0.0157 0.0150
>>> HA 1.4870 1.4590 0.0157 0.0150
>>>
>>> I'm guessing I messed something up here by reloading parameters. Should I
>>> not be creating a new frcmod? Still, I find it weird that two atoms would
>>> have the same type but different parameters. Where does the flag "-at
>>> amber" get parameters from? I assumed these would be the same LJ types
>> that
>>> have been around since FF94.
>>
>>
>>
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>> http://lists.ambermd.org/mailman/listinfo/amber
>
>
>
> --
> ================================ Current Address =======================
> Brian Radak : BioMaPS
> Institute for Quantitative Biology
> PhD candidate - York Research Group : Rutgers, The State
> University of New Jersey
> University of Minnesota - Twin Cities : Center for Integrative
> Proteomics Room 308
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> radakb.biomaps.rutgers.edu
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--
Jason M. Swails
Quantum Theory Project
University of Florida
Ph.D. Candidate
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Received on Wed Jul 03 2013 - 03:00:02 PDT
