If it's a single residue, one way to tell if all the bonds
are there is to edit it in xleap and see. Otherwise, you can
saveamberparm and load prmtop and inpcrd into VMD and see the
same thing.
Bill
> Yes. It's a single residue. I didn't use iwrap. Below is my script
>
> MD run with ntt3 glycam
> &cntrl
> nstlim = 500000, dt=.002,
> irest=1, ntpr=5000, ntwx=5000, ntx=5,
> temp0=298.15, tempi=298.15, ntt=3, gamma_ln=1.0,
> tautp=2.0, taup=0.2, cut=12.0,
> ntb=2, ntp=1,
> ntc=2, ntf=2,
> /
>
> This molecule is in the crystal structure, so I didn't modify anything
> from it. But I used GAFF and antechanber generate its topology and
> coordinate files since leaprc.FF99 doesn't include this molecule.
>
> Thanks
>
> Jason
>
> On 9/28/10, Bill Ross <ross.cgl.ucsf.edu> wrote:
>>> I am running Glycam MD. I found the ligand in the complex separated
>>> into two parts sometimes. Do you know what was the reason? Do I need
>>> connect the atoms in the ligand?
>>
>> Is the ligand a single residue? How did you define it?
>>
>> Bill
>>
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>>
>
>
> --
> Yusheng Jason Jiang
> Department of Chemistry
> Georgia State University
> Atlanta, 30302 GA
>
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Received on Wed Sep 29 2010 - 10:00:12 PDT
