Install new amber force fields ports in Gromacs

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Amber force fields are popular for protein, DNA, RNA and lipid simulations. Recently updated amberff12, amberff14 and amberff15 were reported to perform better than amber99sb and amber99sb-ildn.

Gromacs is a commonly used simulation software, which using OpenMM to enable GPU acceleration. Gromacs is fast and easy to use. A lot of people use amberff in Gromacs.

So to use the newly release amberff12 and amber14sb in gromacs, we need to some work.

Step 1. Install Gromacs 4.6.x or Gromacs 5.0.x or Gromacs 5.1.x

Installation instructions could be find here:
For 4.6.x
http://www.gromacs.org/Documentation/Installation_Instructions_4.6
For 5.0.x and 5.1.x
http://www.gromacs.org/Documentation/Installation_Instructions_5.0

Suppose you are user john, you installed a gromacs 4.6.7 in /home/john/applications/. After installation, you should source the GMXRC by:
source  /home/john/applications/gromacs.4.6.7/GMXRC
And add topology files to environments by:
export GMXLIB=/home/john/applications/gromacs.4.6.7/share/gromacs/top
or add this line in your bashrc (/home/john/.bashrc)

Step 2. Download the amberff ports

We need to download the amberff14sb.tar.gz or amberff12.sb.tar.gz from here:
http://www.gromacs.org/Downloads/User_contributions/Force_fields

Step 3. Copy files to gromacs topology folder

Generally, after you installed gromacs, the topology files of gromacs are stored in
$GMXROOT/share/gromacs/top
So you need to copy the files you download to this location.
Example: cp amber14sb.ff.tar.gz /home/john/applications/gromacs.4.6.7/share/gromacs/top
After which, go to the location and untar the files.
cd /home/john/applications/gromacs.4.6.7/share/gromacs/top
tar xvf amber14sb.ff.tar.gz

Step 4. Modify forcefield.doc

Now you are almost done. Go to the folder amber14sb.ff:
cd  /home/john/applications/gromacs.4.6.7/share/gromacs/top/amber14sb.ff
modify the first line of this file:
vi forcefield.doc
Before modification:
After modification:

Step 5. Test.

Now you could test your amber14sb by using:

pdb2gmx -f yourpdb.pdb -p topol.top -ignh
after which you will be prompted to select a force field:


Now enjoy!

Comments

  1. Unknown15 October 2017 at 12:14

    I see that your pdb2gmx command requires -ignh, which would remove all the waters and then have them reassigned by GROMACS. Would that result in changes in the protonation states of residues in the protein?

    ReplyDelete
    Replies
    1. MemoryDown23 November 2017 at 01:25

      Yes, you are right. In general, we won't do that unless we really don't care about the protonation state.

      Delete
  2. Unknown12 March 2020 at 10:53

    Hi, I am very glad to see your blog post. And I had mentioned that the new version Gromacs (like 2019.03 version)maybe had one bug or something changed about the function of top folder in Gromacs. I followed your methods about forcefield.doc file modification. But it doesn't work now, So which suggestions could you give. Any suggestions are welcome. Thanks a lot.

    ReplyDelete
    Replies
    1. Tegar20 June 2021 at 00:29

      same here.. it seems like it doesn't work in a same wat for the newer version...

      Delete

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