From: Kenno Vanommeslaeghe (kvanomme_at_rx.umaryland.edu)
Date: Tue Sep 30 2014 - 11:37:03 CDT
2 obligatory warnings, both of which have been brought up on this list
several times over the last year or so. I wonder why these things keeps
- You probably don't want to simulate folic acid in isolation, but rather
in interaction with something else, typically a protein. If you wish to
represent the protein by Amber, you should use GAFF/Antechamber for folic
acid and nothing else. If you wish to represent the protein by CHARMM, you
should use CGenFF for folic acid and nothing else. Never mix-and-match
different force fields in the same simulation system! As for DREIDING,
there does not exist a DREIDING protein force field, and it's not even
parameterized towards the liquid phase AFAIK, so I don't think it would be
the right choice for the job.
- Similarly, Swissparam's approach of combining CHARMM L-J
parameters with MMFF94 charges and dihedrals is fundamentally flawed.
While it might be acceptable for the high-throughput applications it is
aimed at (such as force field-base docking), I wouldn't touch it with a
10-foot pole for serious MD work.
On 09/30/2014 11:06 AM, Fotis Baltoumas wrote:
> Hello Haleh,
> As far as I know, by default force fields such as CHARMM or AMBER do not
> have parameters for folic acid or other small molecules. Perhaps more
> generic solutions such as DREIDING may be appropriate.
> However, you can use services such as CGenFF
> (http://mackerell.umaryland.edu/~kenno/cgenff/) or SwissParam
> (http://www.swissparam.ch/), which will generate topology and parameter
> files for any small molecule you submit in CHARMM format.
> Hope I helped,
> Fotis Baltoumas
>> 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
This archive was generated by hypermail 2.1.6 : Thu Dec 31 2015 - 23:21:16 CST