[gmx-users] Generating Glycerol parameters from propanol parameters - OPLS

Andrey Frolov andrey.i.frolov at mail.ru
Mon May 26 09:43:26 CEST 2014

Dear Carlos and gmx-users,
I would recommend to use an automatic tool for assignment of OPLS-AA force filed for small molecules. My experience shows that manual edit of topology files with many atoms is prone to mistakes. One of automatic FF assignment tools for OPLS-AA is the ffld_server of Maestro Schrodinger, which is free for academia (you should register on shcrodinger website and will be able to download it.) To generate OPLS-AA force field you will need only coordinates of atoms of your molecule.
To convert the ffld_server topology to gromacs format you can use a free program ffconv.py: 


After conversion the script can check if the converted topology is good and nothing was screwed up during the conversion. It is evaluated by performing energy calculations by ffld_server and gromacs for given configurations of your molecules.
Apart from that, the ffconv can convert Charmm and Amber force field formats for SMALL molecules (ligands) to gromacs, and some other formats.
So far I used ffconv.py by myself and only recently made much of efforts to make it user-friendly and easy to use. Some examples and documentation is given inside the ffconv_v1.0.tar.gz on the cited webpage. Please give your feedback if you decide to use ffconv.py, this will be very important for me as a developer. Also, if something goes wrong please also let me know: but in this case please give me your input files and show me error messages coming from ffconv.py.
Hope this helps.
Kind regards,

>Message: 6
>Date: Sun, 25 May 2014 12:28:39 -0400
>From: Carlos Navarrro Retamal < cnavarro at utalca.cl >
>To:  gmx-users at gromacs.org < gmx-users at gromacs.org >
>Subject: [gmx-users] Generating Glycerol parameters from propanol
>parameters	- OPLS
>Message-ID: < 8C8A0D6AE98448019D2F6375378D4681 at utalca.cl >
>Content-Type: text/plain; charset="utf-8"
>Dear gromacs users,
>I?m trying to generate the parameters of Glycerol to use them on OPLS.
>I was looking them everywhere without luck, but then i realised that on the folder of OPLS on gromacs are the parameters of propanol.
>So i was wondering, it is ok if i just changed the atoms (at its respective charge) in order to use this parameters in my simulations?
>Is there anything else i should also changed on the .itp file?
>Hope someone can help me,
>Have a nice day.
>Carlos Navarro Retamal
>Bioinformatic engineer
>PhD student in Applied Science, Universidad de Talca, Chile
>Center of Bioinformatics and Molecular Simulations (CBSM)
>Universidad de Talca
>2 Norte 685, Casilla 721, Talca - Chile 
>Tel?fono: 56-71-201 798, 
>Fax: 56-71-201 561
>Email:  carlos.navarro87 at gmail.com or  cnavarro at utalca.cl
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