Dear Ross Walker,
Sorry to send this email to you. It seems the my previous email was not
received by the amber mailing list.
Following your tutorial(
http://ambermd.org/tutorials/basic/tutorial4b/), I
generated parameters for my ligand, which has a group of -CCl3.
After 2 ns equilibration, I found that the bond length for these three
C-Cl bonds is 1.72 , 1.75, 1.84 angstrom, respectively. Is the value 1.84
is normal?
Details of generating parameters and md simulation are as following:
Antechember module from Ambertools 1.3 and AM1-BCC charge was used for the
calculation following your famous tutorial (
http://ambermd.org/tutorials/basic/tutorial4b/) with the same protocol.
After restrained minimization(1000 steps), free minimization(1500 steps),
restraind heating process in NVT ensemble(20ps), I directly equilibrated the
whole system in NPT ensemble for 2ns.
Best regards
Shulin
On Mon, Apr 12, 2010 at 3:26 PM, Shulin Zhuang <shulin.zhuang.gmail.com>wrote:
> Dear All,
>
> I have done simulation of a protein-ligand compelx in NPT ensemble at 300
> degree. In this ligand, there is a CCl3 group. Antechember module from
> Ambertools 1.3 was used to generate the parameter for the ligand following
> the tutorial of Dr. Ross Walker:
> http://ambermd.org/tutorials/basic/tutorial4b/ using AM1-BCC charge.
>
> After restrained minimization(1000 steps), free minimization(1500 steps),
> restraind heating process in NVT ensemble(20ps), I directly equilibrated the
> whole system in NPT ensemble for 2ns.
>
> I used VMD 1.87 to check the ligand and found that before the NPT
> equilibration, the ligand is well, however, during the equilibration, the
> bond length of C-Cl varies, sometimes around 1.75 angstrom, sometimes above
> 1.8 angstrom. If this bond length above 1.8 angstrom, for example 1.84
> angstrom, the VMD would not treat it as a bond.
>
> Is the variation of C-Cl bond length normal? Any suggestions would be
> much appreciated!
>
> Best regards
> Shulin
>
>
>
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Received on Tue Apr 13 2010 - 11:30:06 PDT
