> GLC = sequence { ROH 0GA }
is not guaranteed to spare you from steric overlap. You could savepdb on that and clean it up in your favorite editor, or, since it's only 2 residues, you could try it in xleap ('edit GLC').
Bill
On 11/14/17 7:14 AM, Aashish Bhatt wrote:
> I followed the step
>
> tleap -s -f leaprc.GLYCAM_06j-1
> GLC = sequence { ROH 0GA }
> check GLU
> saveoff GLC glc.lib
> saveamberpam GLC glc.prmtop glc.inpcrd
> savepdb GLC glc.pdb
> quit
>
>
>
> On Tue, Nov 14, 2017 at 8:33 PM, Carlos Simmerling <
> carlos.simmerling.gmail.com> wrote:
>
>> The existence of a bond isn't likely due to the charges. We don't know how
>> you set up all of the other parameters though, so it's hard to help.
>>
>> On Nov 14, 2017 9:48 AM, "Aashish Bhatt" <aashish.ph16221.inst.ac.in>
>> wrote:
>>
>>> Dear Sir/Ma'am
>>>
>>> I have performed glucose dynamics in vacuum using parameter
>>> (Mulliken,Lowedin,ESP,RESP and 0GA+ROH charges) that i got from orca and
>>> Gaussian dft optimization of glucose molecule. In gas phase dynamics i
>> have
>>> found that the anomeric OH group is showing bonding to O(5) atom.
>>> I am not able to understand the reason behind this binding. I have also
>>> attached screenshot of glucose molecule.
>>>
>>> Regards
>>> Aashish Bhatt
>>> PhD Scholar
>>> INST, Mohali
>>> India
>>>
>>> _______________________________________________
>>> AMBER mailing list
>>> AMBER.ambermd.org
>>> http://lists.ambermd.org/mailman/listinfo/amber
>>>
>>>
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Received on Tue Nov 14 2017 - 07:30:04 PST
