VMD-L Mailing List
From: Peterson J (peterson.jjjj_at_gmail.com)
Date: Mon May 20 2013 - 13:03:57 CDT
- Next message: John Stone: "Re: Obtain solvent-accessible surface vertices"
- Previous message: Anurag Sharma: "error in merging two structures"
- Next in thread: Bennion, Brian: "RE: Suggestions on parameterizing a ligand to simulate in NAMD"
- Reply: Bennion, Brian: "RE: Suggestions on parameterizing a ligand to simulate in NAMD"
- Reply: Jiawei Xu: "Re: Suggestions on parameterizing a ligand to simulate in NAMD"
- Reply: Mayne, Christopher G: "Re: Suggestions on parameterizing a ligand to simulate in NAMD"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]
Hi VMD and NAMD users,
I'm very new to VMD and NAMD. I'm now in the process of parameterizing a
ligand molecule. As I came across various a few web tools like paramchem,
swissparam and so on. I have also seen VMD providing a plugin called
Forcefield Toolkit calculating parameters using Gaussian and preparing the
files for MD run using NAMD.
I would like to get a few suggestion points on which one to use and the
advantages and disadvantages over one another.
What if I use one of the mentioned webtools instead of ffTk that use
lengthy QM calculations to obtain the parameters?
Thanks in advance for the suggestions.
-Peterson
- Next message: John Stone: "Re: Obtain solvent-accessible surface vertices"
- Previous message: Anurag Sharma: "error in merging two structures"
- Next in thread: Bennion, Brian: "RE: Suggestions on parameterizing a ligand to simulate in NAMD"
- Reply: Bennion, Brian: "RE: Suggestions on parameterizing a ligand to simulate in NAMD"
- Reply: Jiawei Xu: "Re: Suggestions on parameterizing a ligand to simulate in NAMD"
- Reply: Mayne, Christopher G: "Re: Suggestions on parameterizing a ligand to simulate in NAMD"
- Messages sorted by: [ date ] [ thread ] [ subject ] [ author ] [ attachment ]