[gmx-users] some questions about gromacs

#NGUYEN CONG TRI# NGUY0045 at ntu.edu.sg
Mon Oct 6 13:18:50 CEST 2008


1. Yes you can, please refer to this 
There is a script to convert amber formats into gromacs format. You can get it from here 
It is only tested for small molecules although it should work for bigger system.

2. Normally you have to run geometry optimization using a QM package (Gaussian or Gamess; Gamess is free. Sometimes they can give different results, though) at B3LYP/6-31G* level (I think this level is enough for most cases). Then calculate ESP at level HF/6-31G* and derive the RESP charge using Antechamber if your molecule is simple. Finally, you need to judge and add in mixing parameters bases on similar structure. Gaff and Antechamber can do this step for you if your molecule is simple enough. That's for preparing parameters for your molecules in Amber force field. 

3. Nothing other than reading lots and experiencing yourself :).

Good luck!!!


-----Original Message-----
From: gmx-users-bounces at gromacs.org on behalf of dcip1101
Sent: Mon 10/6/2008 5:52 PM
To: gmx-users at gromacs.org
Subject: [gmx-users] some questions about gromacs
 Dear all,
  I am a new user of Gromacs. To start my job, I am confused by several questions about GROMACS and requesting the answers.
1. Can one use amber force field in gromacs?
2. How to prepare parameters for a cofactor not included in the standard force fields?
3. Any further suggestions to a new user to use the package better?
Thanks so much for your time.
Have a nice day.

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