[gmx-users] adding metal-bonding parameters to a force field

[Justin Lemkul]

On 4/1/14, 8:49 AM, Ahmet yıldırım wrote:
> There are both Zn-OH(zinc-hydroxyl) and Zn-H2O (zinc-water) bond in
> structure, then should I modify "aminoacids.hdb" and "aminoacids.rtp" to
> add OH (hydroxyl) and water parameters?
>
>

The parameters listed in Table 1 need to be added to ffbonded.itp and 
ffnonbonded.itp.  The thing to watch out for is that there are two different 
H-O-H angles that are defined, depending on whether the water is free or bound 
to Zn.  Therefore, you need unique atomtypes to differentiate between different 
types of water, so that requires modification of atomtypes.atp, as well, if you 
will be processing the structure with pdb2gmx.

Table 2 corresponds to a specific residue that needs to be added as an .rtp 
entry (again, only if you are using pdb2gmx to create the topology).  The .hdb 
entry is only necessary if you do not have H positions in the input coordinate file.

-Justin

> 2014-04-01 11:03 GMT+03:00 Ahmet yıldırım <ahmedo047 at gmail.com>:
>
>> Firstly, I will change ffnonbonded.itp and ffbonded.itp. Later?
>>
>>
>> 2014-04-01 10:37 GMT+03:00 Ahmet yıldırım <ahmedo047 at gmail.com>:
>>
>> Dear users,
>>>
>>> Please see the file from the link:
>>>
>>> http://www.google.com.tr/url?sa=t&rct=j&q=&esrc=s&source=web&cd=1&cad=rja&uact=8&ved=0CC0QFjAA&url=http%3A%2F%2Fpubmedcentralcanada.ca%2Fpicrender.cgi%3Fartinstid%3D1482211%26blobname%3DNIHMS61946-supplement-File002.pdf&ei=DGs6U560PMHxhQejyIDABg&usg=AFQjCNGUfMCQZYegoRpLGg5D9GjpFsPCxQ&sig2=vr6-1syRClNsDmFdMlWyXw&bvm=bv.63934634,d.ZG4
>>>
>>> I want to add table 1 and table 2 parameters to amber force field. How can
>>> I achieve it?
>>>
>>> --
>>> Ahmet Yıldırım
>>>
>>
>>
>>
>> --
>> Ahmet Yıldırım
>>
>
>
>

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

Justin A. Lemkul, Ph.D.
Ruth L. Kirschstein NRSA Postdoctoral Fellow

Department of Pharmaceutical Sciences
School of Pharmacy
Health Sciences Facility II, Room 601
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalemkul at outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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