Hello, I'm very intreresting in this question, so can I join in ?
First, I wonder if there is "interactions" between hydrophbic residues. what I
know is that for those nonpolar residues, their interactions with water is
weaker than the polar attractions between two water molecules, so that
I'm sorry I need to correct the first point in my last e-mail. I mean I wonder
if it is the "hydrophobic interaction" that make those hydrophobic residues
together. Maybe what really gather those hydrophbic ones is Wan der Vaals force
plus the "squeezing out" force from water.
At
I wish I could offer some help. br/I used to prepare small compound
molecules, and the ligand.frcmod was generated by parmchk of AMBER. The
ligand.frcmod was then handed to tleap or xleap of AMBER, to generate
ligand.prmtop and ligand.inpcrd. Following that, a python script called
acpype.py
changing to a more
matchable forcefield.
Thanks to Justin! You help me a lot!
在 2015-05-11 19:46:27，Justin Lemkul jalem...@vt.edu 写道：
On 5/10/15 8:48 PM, 范聪 wrote:
Hello everyone!
I offered a picture called ask.png to illistrate my question.
According to the referense papers, the H
It's so kind of you to answer my question in such a short time. I'll try other
forcefields. Thank you very much!
在 2015-05-11 19:46:27，Justin Lemkul jalem...@vt.edu 写道：
On 5/10/15 8:48 PM, 范聪 wrote:
Hello everyone!
I offered a picture called ask.png to illistrate my question.
According
Hello, can you treat HYL as ligand and build its forcefield parameters
referring to this link
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin/gmx-tutorials/complex/index.html
At 2015-05-11 08:39:39, Ming Tang m21.t...@qut.edu.au wrote:
Dear all,
I want to simulate a protein containing
Hello, as to this situation, what I often do is to open the pdb file with
editing software such as schrodinger or SYBYL, then mutate the incomplete
residue to a complete one. Also, in these software, there will be a protein
preparation wizard to help you check and repair the protein structure.
