[gmx-users] Forcefield parameters for AcetylCoA

[Justin A. Lemkul]

Please keep the discussion on the gmx-users mailing list.

On 7/11/12 10:43 AM, panbazha wrote:
> Dear Justin,
> That file was generated by me in ATB, The issue is when i looked into
> the united atom itp file, I found many bonds and angles has not determined. So,
> just wondering if there are any published reports to edit it manually.
>

A quick literature search should turn something up.  Google returns lots of 
results if you search "Gromos96 acetyl CoA" (without the quotes).

I looked at the missing bonded parameters and they should all be quite easy to 
define based on known values in ffbonded.itp - it is not clear to me why they 
are missing.  Most, if not all, of the missing bonds are between OA and H atoms, 
which are simple alcohol groups (bond type gb_1).

-Justin

> Best regards
>
>
>
>
>
> Quoting "Justin A. Lemkul" <jalemkul at vt.edu>:
>
>>
>>
>> On 7/11/12 8:18 AM, Padmanabhan Anbazhagan wrote:
>>> Dear All,
>>> Could anyone please suggest me some article or information that contains
>>> force field parameters (gromacs53A6) for acetyl Coenzyme A
>>>
>>
>> Google turned up:
>>
>> http://compbio.biosci.uq.edu.au/atb/download.py?molid=5470
>>
>> -Justin
>>
>> --
>> ========================================
>>
>> Justin A. Lemkul, Ph.D.
>> Research Scientist
>> 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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>
>
>
>

-- 
========================================

Justin A. Lemkul, Ph.D.
Research Scientist
Department of Biochemistry
Virginia Tech
Blacksburg, VA
jalemkul[at]vt.edu | (540) 231-9080
http://www.bevanlab.biochem.vt.edu/Pages/Personal/justin

========================================