From: Haleh a (halehabdi_at_sabanciuniv.edu)
Date: Wed Oct 01 2014 - 01:42:20 CDT
Thank you all for the helpful replies.
On Tue, Sep 30, 2014 at 7:37 PM, Kenno Vanommeslaeghe <
kvanomme_at_rx.umaryland.edu> wrote:
> 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
> popping up...
>
> - 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.
> http://www.ks.uiuc.edu/Research/namd/mailing_list/
> namd-l.2013-2014/0846.html
> http://www.ks.uiuc.edu/Research/namd/mailing_list/
> namd-l.2013-2014/0893.html
> http://www.ks.uiuc.edu/Research/namd/mailing_list/
> namd-l.2013-2014/1250.html
>
>
>
> 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
>>>
>>>
>>
>>
>
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