[gmx-users] filling missing param values

[gromacs query]

Dear Justin,

>>   Parameterization is a hard road that takes a lot of time

I agree and thanks for reply



On Thu, Jul 25, 2013 at 3:47 PM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 7/25/13 8:41 AM, gromacs query wrote:
>
>> Dear Justin,
>>
>> Thanks this paper is quite explained and requires much detailed study
>> (sorry am escaping!)
>> As I have these two params missing, is there any tool that can help me in
>> this regard or may be some approximation method I may use?
>>
>>
> It is very hard to assign dihedrals based on approximations, and they are
> generally not very transferable.  Bonds and angles are easier, but
> dihedrals are quite complex and the types and charges on atoms i and l have
> a significant impact on the parameters.  Shortcuts here will probably lead
> to a bad topology.  Parameterization is a hard road that takes a lot of
> time, even for bonded terms that you think may be simple.
>
> -Justin
>
>  thanks
>>
>>
>> On Thu, Jul 25, 2013 at 3:28 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>
>>>
>>> On 7/25/13 8:25 AM, gromacs query wrote:
>>>
>>>  Dear All,
>>>>
>>>> I am working on some molecule and I have defined atom types with OPLSaa
>>>> and
>>>> all atom types really exist in oplsaa and well chosen so no
>>>> approximation
>>>> in choosing atom types. During grompp, I found there are dihedral param
>>>> missing. e.g.
>>>> N CT CT NT
>>>> N CT CT N3
>>>>
>>>> Is there any 'good' way of finding/assuming dihedral params for this?
>>>> or I
>>>> should choose values of some nearby atom types?
>>>>
>>>>
>>>>  The OPLS dihedral fitting strategy is exceptionally well explained in
>>> the
>>> Kaminski 2001 paper (reference in Gromacs manual).
>>>
>>> -Justin
>>>
>>> --
>>> ==============================****====================
>>>
>>>
>>> Justin A. Lemkul, Ph.D.
>>> 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 <jalemkul at outerbanks.**
>>> umaryland.edu <jalemkul at outerbanks.umaryland.edu>> | (410)
>>> 706-7441
>>>
>>> ==============================****====================
>>>
>>> --
>>> gmx-users mailing list    gmx-users at gromacs.org
>>> http://lists.gromacs.org/****mailman/listinfo/gmx-users<http://lists.gromacs.org/**mailman/listinfo/gmx-users>
>>> <htt**p://lists.gromacs.org/mailman/**listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
>>> >
>>> * Please search the archive at http://www.gromacs.org/**
>>> Support/Mailing_Lists/Search<h**ttp://www.gromacs.org/Support/**
>>> Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>>before
>>> posting!
>>>
>>> * Please don't post (un)subscribe requests to the list. Use the www
>>> interface or send it to gmx-users-request at gromacs.org.
>>> * Can't post? Read http://www.gromacs.org/****Support/Mailing_Lists<http://www.gromacs.org/**Support/Mailing_Lists>
>>> <http://**www.gromacs.org/Support/**Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>>> >
>>>
>>>
> --
> ==============================**====================
>
> Justin A. Lemkul, Ph.D.
> 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 <jalemkul at outerbanks.umaryland.edu> | (410)
> 706-7441
>
> ==============================**====================
> --
> gmx-users mailing list    gmx-users at gromacs.org
> http://lists.gromacs.org/**mailman/listinfo/gmx-users<http://lists.gromacs.org/mailman/listinfo/gmx-users>
> * Please search the archive at http://www.gromacs.org/**
> Support/Mailing_Lists/Search<http://www.gromacs.org/Support/Mailing_Lists/Search>before posting!
> * Please don't post (un)subscribe requests to the list. Use the www
> interface or send it to gmx-users-request at gromacs.org.
> * Can't post? Read http://www.gromacs.org/**Support/Mailing_Lists<http://www.gromacs.org/Support/Mailing_Lists>
>