[gmx-users] GAAMP parameterization

[Mohsen Ramezanpour]

Thanks Justin.

I used CGenFF as initial parameters and the output file from GAAMP was not
good.
By "not good" I mean that:
the QM PS was not matched with the fitted parameters. In fact, the relative
depth of local minima and even the location of minima was not the same as
the QM one.

When I use GAFF as initial parameters, everything is fine and all the
dihedrals have been fitted to the QM PS.
So, I thought maybe I could use these charges and dihedral parameters
instead.

Cheers,
Mohsen



On Tue, May 2, 2017 at 9:50 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 5/2/17 11:46 AM, Mohsen Ramezanpour wrote:
>
>> Hi David,
>>
>> My bad.
>> GAAMP server is a server (developed by Dr. Roux at Chicago university)
>> which does an automated QM calculations for charge and dihedral fitting
>> for
>> both Amber and Charmm36 ff.
>> Just to start, it takes the initial parameters from either GAFF or CGenFF
>> and tries to make them optimized.
>> Here is the link for others who might be interested:
>>
>> http://gaamp.lcrc.anl.gov/
>>
>> I read the article but I still do not know the answer for the questions I
>> asked.
>>
>>
> GAFF parameters are to be used with AMBER, CGenFF with CHARMM.  So if you
> used GAFF to try to parametrize something ultimately for use with CHARMM, I
> wouldn't use it.  Do it properly with CGenFF.  Note that the CGenFF server
> is still operable and you should get a result almost immediately.  That
> doesn't mean it won't still need some work, but all the target data from
> GAAMP (e.g. the QM) is still valid for refining the topology.
>
> -Justin
>
>
> Cheers,
>> Mohsen
>>
>>
>> On Mon, May 1, 2017 at 11:06 PM, David van der Spoel <
>> spoel at xray.bmc.uu.se>
>> wrote:
>>
>> On 02/05/17 06:06, Mohsen Ramezanpour wrote:
>>>
>>> Hi Everyone,
>>>>
>>>> I would like to know your opinion on these questions.
>>>>
>>>> I highly appreciate your comments in advance.
>>>>
>>>> You could at least at the address of the server and tell in one line
>>> what
>>> it is supposed to do.
>>>
>>> You should never mix force fields unless you really really know what you
>>> are doing. Not even change water models - most people trying that don't
>>> really know what they are doing.
>>>
>>>
>>>> Cheers,
>>>> Mohsen
>>>>
>>>> On Thu, Apr 27, 2017 at 10:23 PM, Mohsen Ramezanpour <
>>>> ramezanpour.mohsen at gmail.com> wrote:
>>>>
>>>> Dear Gromacs users,
>>>>
>>>>>
>>>>> Using GAAMP server for parameterization, if the GAFF for
>>>>> "initial parameters" is used instead of "CGenFF":
>>>>>
>>>>> 1) Can the results still be used for using simulation in "Charmm36"
>>>>> force
>>>>> field? Assuming that all the other values are chosen as default ones in
>>>>> the
>>>>> GAAMP webpage.
>>>>>
>>>>> 2) Will the result be the same (or approximately the same) with when
>>>>> "CGenFF" is used as initial parameters?
>>>>>
>>>>> 3) Will the units for angles, dihedrals, distances, ... be in CGenFF or
>>>>> GAFF? I was wondering if I can still use the cgen_charmm2gmx.py script
>>>>> for
>>>>> conversions to use it in Gromacs package?
>>>>>
>>>>> As I understood from the paper, GAAMP can give output for
>>>>> parameterization
>>>>> in both Charmm and Amber force fields.
>>>>>
>>>>> This could be easily tested by running the same job two times.
>>>>> Unfortunately, GAAMP server has some problems at the moment so it will
>>>>> take
>>>>> too much time to check this.
>>>>>
>>>>> I appreciate your comments in advance.
>>>>>
>>>>> Best,
>>>>> Mohsen
>>>>>
>>>>>
>>>>> --
>>>>> *Rewards work better than punishment ...*
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>> --
>>> David van der Spoel, Ph.D., Professor of Biology
>>> Head of Department, Cell & Molecular Biology, Uppsala University.
>>> Box 596, SE-75124 Uppsala, Sweden. Phone: +46184714205.
>>> http://www.icm.uu.se
>>> --
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>>
>>
>>
> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
> Health Sciences Facility II, Room 629
> 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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-- 
*Rewards work better than punishment ...*