Dear Shahid,
> Are the ff libraries in these F-90/91 REDDB projects compatible with the
> new FF ff14SB? Or one has to use the old ff99SB?
F-90: for the Cornell et al. FF & its successive adaptations -> this
is written in the abstract
F-91: for the Duan et al. FF -> this is written in the abstract
My understanding is that all these Stony-Brook FF FF99SB, FF12SB,
FF14SB ... FF99SB ;-) are based on the Cornell et al. FF.
I just checked in the Amber manual 14 page 29:
3.1. Specifying which force field you want in LEaP
File name Original Charge Scheme
leaprc.ff14SB Cornell et al., 1994
regards, Francois
> On Tue, Mar 3, 2015 at 10:18 AM, FyD <fyd.q4md-forcefieldtools.org> wrote:
>
>> Dear Francesca,
>>
>> You might be interested in the F-90 REDDB project:
>> http://q4md-forcefieldtools.org/REDDB/projects/F-90/
>> http://q4md-forcefieldtools.org/REDDB/projects/F-90/script1.ff
>>
>> NADP+ (and far more) is included...
>>
>> regards, Francois
>>
>>
>> > I am running MD of a protein with NADP+ as cofactor.
>> >
>> > I have some troubles with the cofactor parametrization:
>> > antechamber is not recognizing the charge of my mol2 file and as
>> > well pdb file.
>> > So I decided to dowload the prep and frcmod files from Amber
>> > parameter database
>> > but I don't know how to integrate them with my mol2 or pdb file.
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Received on Tue Mar 03 2015 - 05:00:02 PST
