VMD-L Mailing List

From: Bennion, Brian (Bennion1_at_llnl.gov)
Date: Mon May 20 2013 - 14:15:26 CDT

Hello

It totally depends on how unique your ligand is.

If it contains a lot of atom types and bonded interactions that are similar to already parameterized compounds your job will be easier.

Most of the services only do matching to the cgenff for similar interactions. paramchem is nice in that it gives you a score for the matches it makes.

fftk is completely based on qm and mm calculations but it is the only route if you have a fairly unique molecule. its learning curve is a little steep, but the video tutorials help a lot.

Brian

________________________________
From: owner-vmd-l_at_ks.uiuc.edu [owner-vmd-l_at_ks.uiuc.edu] on behalf of Peterson J [peterson.jjjj_at_gmail.com]
Sent: Monday, May 20, 2013 11:03 AM
To: vmd-l_at_ks.uiuc.edu; namd-l_at_ks.uiuc.edu
Subject: vmd-l: Suggestions on parameterizing a ligand to simulate in NAMD

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