[gmx-users] Re: Gromacs
Anton Feenstra (Thuis)
feenstra at few.vu.nl
Thu Feb 22 17:18:27 CET 2007
jacopo.sgrignani at unifi.it wrote:
> I read this email in the mail list of gromacs.
> I have the same problem with my molecules, I created a .itp file using
> PRODRG but I want to use OPLS force field.
> In this mail you said that I can change only atom type and the program
> will change the other data.
> Could you help me with the procedure to do it, please.
I am sorry, but there is not a clear procedure to follow.
In fact, you are extending the forcefield by providing parameters for
another molecule. In principle this should involve rigorous testing and
tuning, e.g. to get correct densities, heat of vaporization,
partitioning and/or other binding constants.
In practice, you may get away by choosing from the available OPLS atom
types. Have a look at the ffoplsbon.itp file to see which atom types you
can pick from, and in ffopls.rtp for how they are used in, e.g.,
proteins (and some other common solvents & assorted molecules).
You can, for example, copy parameters from a phenylalanine sidechain to
use as an aromatic group in your molecule.
| | |
| _ _ ___,| K. Anton Feenstra |
| / \ / \'| | | IBIVU/Bioinformatics - Vrije Universiteit Amsterdam |
|( | )| | | De Boelelaan 1083A - 1081 HV Amsterdam - Netherlands |
| \_/ \_/ | | | Tel +31 20 59 87783 - Fax +31 20 59 87653 - Room P440 |
| | Feenstra at few.vu.nl - www.few.vu.nl/~feenstra/ |
| | "I Live the Life They Wish They Did" (Tricky) |
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