[AMBER] Is the variation of C-Cl bond length normal?

From: Shulin Zhuang <shulin.zhuang.gmail.com>
Date: Mon, 12 Apr 2010 15:26:12 -0700

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-CCl 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

Best regards

On Mon, Apr 12, 2010 at 12:30 PM, Dean Cuebas

> Dear amberers,
> I guess my question is more to Ross Walker, since he is the one whose
> parameterized NAD+ files I am referring to, but I'll accept a clarification
> from anyone! :-)
> Using the .mol2 file with charges and amber atomtypes for NAD+ with parmchk
> and the parm99.dat file, a frcmod file is created that contains improper
> dihedrals for the aromatic adenine ring system. Yet, in the frcmod file
> provided by Ross Walker, there are no such improper dihedrals specified.
> First let me say that I am not implying a mistake on Ross's part, because
> I've seen a few other instances where this is the case also.
> So my question is, when are the impropers that are supplied in the frcmod
> file produced by parmchk not necessary?
> For example, I have a compound I am parameterizing that contains planar
> amides and planar thioester linkages. Using parmchk with the parm99.dat
> file
> gives me impropers in the frcmod file with for each of these, with a large
> force constant of 10.5.
> Do I need these specifications for these planar linkages??
> How do you decide???
> Thanks so very much for your help in advance.
> With regards,
> Dean
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Received on Mon Apr 12 2010 - 15:30:04 PDT
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