From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Tue Sep 30 2014 - 10:43:21 CDT
Folic acid should be excellently supported by CGenFF; you can get CGenFF
topology and parameters for arbitrary molecules at cgenff.paramchem.org
Here are usage instructions (including some NAMD tips):
http://mackerell.umaryland.edu/~kenno/cgenff/program.html
Just be careful with protonation states when preparing your input; there
are 2 ionizable carboxylate groups that should probably be deprotonated,
and there is one aniline-type amine in the linker between the 2 aromatic
rings that would be neutral in isolation but may prefer to be protonated
when occurring in a molecule that would otherwise have a -2 net charge.
The environment in which you wish to simulate also plays a role.
It is usually a good idea to perform some validation and/or refinement on
the high-penalty parts of the output of the CGenFF program at
paramchem.org . Among other tools, FFTK is suitable for that purpose.
However, in the specific case of folic acid, it may not be necessary.
On 09/30/2014 09:44 AM, Haleh a wrote:
> Dear All,
>
> Is there anybody out there who might have the force field parameters for
> folic acid?
> Any help is highly appreciated.
>
> Best regards,
> Haleh Abdizadeh
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