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 - 07:30:04 PDT
