Dear Hannes,
By the way, what is the difference between the dihedral and improper
dihedral like in the 1-4 scaling factos?
Dongshan
On Thu, Mar 27, 2014 at 6:01 PM, Dongshan Wei <dswei0523.gmail.com> wrote:
> 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.
>>
>> _______________________________________________
>> AMBER mailing list
>> AMBER.ambermd.org
>> http://lists.ambermd.org/mailman/listinfo/amber
>>
>
>
>
> --
> ---------------------------------------------------------
> 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
> ---------------------------------------------------------
>
--
---------------------------------------------------------
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
---------------------------------------------------------
_______________________________________________
AMBER mailing list
AMBER.ambermd.org
http://lists.ambermd.org/mailman/listinfo/amber
Received on Thu Mar 27 2014 - 03:30:03 PDT
