You can try only one residue not two, and then generate the topology file again.
On Sep 29, 2010, at 9:07 AM, Jiang Yusheng wrote:
> 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 - 07:30:06 PDT
