[gmx-users] GAAMP parameterization

[Justin Lemkul]

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

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