Speaking of Halloween, I'm now binding neurons in a slightly similar,
mild manner:
http://phobrain.com/pr/home/gallery/pair_horiz_stairs_pair_railing_tubes_corner_shadow.jpg
Bill
On 10/31/18 2:30 AM, Bill Ross wrote:
> Coming on this cold with a Sherlock Holmes approach and vestigial
> awareness of chemistry (i.e. Dave's issue and your response), an obvious
> possibility is that the frcmod.ff14SB file you added the params to is
> not the one you are loading. Try listing the param in leap, or some
> addition or deletion experiment to prove to yourself that you are
> loading the right file, then burn this message and fly into the night. :-)
>
> Bill
>
>
> On 10/31/18 2:13 AM, Rajbinder Kaur Virk wrote:
>> Hello
>>
>> This missing parameters is probably due the presence of gamma glutamic acid
>> as one of the amino acid in the peptide and it is forming a gamma linkage
>> as peptide bond. As discussed earlier, I tried to make .lib file, after
>> saving by xleap, the pdb seems to be right but prmtop and inpcrd files are
>> not being saved.
>>
>> Following changes were made in the frcmod.ff14SB file:
>> Angle
>> O2-C -N 72.7 120.63
>> IMPR
>> CT-O2-C-N 10.5 180. 2.
>>
>> Please provide some suggestions....we are really stuck. Thank you
>>
>> Thank you
>> With regards
>> Rajbinder Kaur Virk
>>
>>
>> On Wed, Oct 31, 2018 at 7:11 AM David Case <david.case.rutgers.edu> wrote:
>>
>>> On Tue, Oct 30, 2018, Rajbinder Kaur Virk wrote:
>>>> Could not find angle parameter: O2 - C - N
>>>>
>>>> thereafter i tried to provide the required parameters in the .dat file
>>>> itself (frcmod.ff14SB), still the parameter are not being recognized and
>>>> the error persists.
>>> Can you show the exact changes to the frcmod.ff14SB file you made, plus all
>>> the commands you gave to tleap?
>>>
>>> As an aside, you should generally not edit frcmod.ff14SB itself, but rather
>>> make a new frcmod file--that way you won't mess up other runs that expect
>>> to
>>> have the un-modified frcmod.ff14SB file.
>>>
>>> Second aside: there are indeed no O2-C-N angles in ordinary proteins. Are
>>> you
>>> sure you have correct atom types?
>>>
>>> ....dac
>>>
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>
> _______________________________________________
> AMBER mailing list
> AMBER.ambermd.org
> http://lists.ambermd.org/mailman/listinfo/amber
>
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Wed Oct 31 2018 - 03:00:02 PDT
