Dear Hannes,
I'm sorry for urging an answer in this community.
I set up the trp-cage protein in Amber 12 using the same method with
tutorail 3 except a ff99SB FF instead of ff99 FF. Then I got the
topological and coordinate files and in the top file, I found three of 37
SCEE and SCNB values are 0.0. I considered to use DL_FIELD to do the FF
conversion, but I found DL_FIELD just can deal with the Amber ff03 force
field. So I decided to write a code.
Best!
Dongshan
On Thu, Mar 27, 2014 at 5:24 PM, Hannes Loeffler <Hannes.Loeffler.stfc.ac.uk
> wrote:
> On Thu, 27 Mar 2014 17:06:35 +0800
> Dongshan Wei <dswei0523.gmail.com> wrote:
>
> > why nobody answers this question?
>
> Maybe because your original email arrived in my mailbox at 03:04 GMT
> which I think is something like 8pm in California? Not everybody is
> in front of their computer when you do. Allow at least about 24h of
> turn around time. You already started complaining after merely 6h!
>
> I do not know how you have created your parmtop and why the scaling
> factors would be zero but have you considered or are you already using
> DL_FIELD for this job?
>
> Cheers,
> Hannes.
>
> > On Thu, Mar 27, 2014 at 11:04 AM, Dongshan Wei <dswei0523.gmail.com>
> > wrote:
> >
> > > Hi Everyone,
> > >
> > > I'm converting the Amber force field to DL_POLY force field for
> > > Trp-cage protein. I dealed with the Amber ff99SB FF, I found in
> > > the .prmtop file, the "SCEE_SCALE_FACTOR" and "SCNB_SCALE_FACTOR"
> > > for some dihedral angles are 0.0. If the SCEE factor is 0.0, it
> > > means the actually scaling is 1.0/0.0 infinitely. So how to
> > > understand the 0.0 factor? Thakns!
> > >
> > > Best!
> > >
> > > Dongshan
> > >
> > > --
> > > ---------------------------------------------------------
> > > Dongshan Wei, Dr.
> > > Chongqing Institute of Green and Intelligent Technology, CAS
> > > 266 Fangzheng Ave, Beibei District, Chongqing 400714, China
> > > Email: dswei.cigit.ac.cn <dswei.cigit.cas.cn>
> > > Phone: (+86) 23-65935641
> > > ---------------------------------------------------------
> > >
> >
> >
> >
>
> --
> Scanned by iCritical.
>
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>
--
---------------------------------------------------------
Dongshan Wei, Dr.
Chongqing Institute of Green and Intelligent Technology, CAS
266 Fangzheng Ave, Beibei District, Chongqing 400714, China
Email: dswei.cigit.ac.cn <dswei.cigit.cas.cn>
Phone: (+86) 23-65935641
---------------------------------------------------------
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Received on Thu Mar 27 2014 - 03:30:02 PDT
