[gmx-users] Trehalose RTP file trouble

[Tsjerk Wassenaar]

Hi,

The sugars were improved in 45a3. The parameters haven't changed for
the later versions.

Cheers,

Tsjerk

On Tue, Apr 13, 2010 at 12:24 AM, Justin A. Lemkul <jalemkul at vt.edu> wrote:
>
>
> Michael McGovern wrote:
>>
>> Hi everyone.  I'm doing some simulations involving the sugar trehalose,
>> with the 53a6 force field.  There is an odd issue I am having with the rtp
>> file for trehalose.  It seems to be charged.  Here is the beginning of the
>> rtp entry:
>>
>>  [ TRH ]
>>  [ atoms ]
>>  HO4     H     0.41000     0
>>   O4    OA    -0.64200     0
>>   C4   CH1     0.23200     0
>>   C3   CH1     0.23200     1
>>   O3    OA    -0.64200     1
>>  HO3     H     0.41000     1
>>   C2   CH1     0.23200     2
>>   O2    OA    -0.64200     2
>>  HO2     H     0.41000     2
>>   C6   CH1     0.23200     3
>>   O6    OA    -0.64200     3
>>  HO6     H     0.41000     3
>>   C5   CH1     0.37800     4
>>   O5    OA    -0.45000     4
>>   C1   CH1     0.24200     4
>>   O1    OA    -0.34000     4
>>  C1'   CH1     0.24200     4
>>  O5'    OA    -0.45000     4
>>  C5'   CH1     0.37800     4
>>  C4'   CH1     0.27500     5
>>  O4'    OA    -0.60000     5
>>  HO4'     H     0.47000     5
>>  C3'   CH1     0.23200     6
>>  O3'    OA    -0.64200     6
>>  HO3'     H     0.41000     6
>>  C2'   CH1     0.23200     7
>>  O2'    OA    -0.64200     7
>>  HO2'     H     0.41000     7
>>  C6'   CH1     0.23200     8
>>  O6'    OA    -0.64200     8
>>  HO6'     H     0.41000     8
>>
>> Charge group 5 has a net charge of +0.145.  Is this a typo?  Should I just
>> change it to be the same as the other C-O-H charge groups?
>>
>>
>
> The net charge certainly seems wrong.  Before making any ad hoc changes,
> though, refer to the primary literature for the force field and make sure
> everything else is right.  I think 53a6 has the same charges as 45a4,
> wherein the sugar parameters were improved from 45a3.  I don't see any
> mention of modifications to sugars in the 53a6 paper.  45a4 ref:
>
> Lins and Hunenberger (2005) J Comput Chem 26: 1400-1412.
>
> -Justin
>
> --
> ========================================
>
> Justin A. Lemkul
> Ph.D. Candidate
> ICTAS Doctoral Scholar
> MILES-IGERT Trainee
> Department of Biochemistry
> Virginia Tech
> Blacksburg, VA
> jalemkul[at]vt.edu | (540) 231-9080
> http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin
>
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-- 
Tsjerk A. Wassenaar, Ph.D.

post-doctoral researcher
Molecular Dynamics Group
Groningen Institute for Biomolecular Research and Biotechnology
University of Groningen
The Netherlands