[gmx-users] Re :Using FFTK generated parameter file for Protein-Ligand simulations

[Justin Lemkul]

On 3/18/16 6:52 PM, Soumya Lipsa Rath wrote:
> Dear Justin,
>   I have used CGenFF for CHARMM. However, I am not able to understand how to
> include the topology of inhibitor to start a simulation. The metal ions
> which I had talked about are FL and BR and I have got their parameters
> already from CHARMM. I am relatively new to gromacs, I just wanted to know
> how to start a protein-ligand simulation andd how to incorporate the ligand
> parameters.
>

We wrote a converter to interface the CGenFF server with GROMACS:

http://mackerell.umaryland.edu/charmm_ff.shtml#gromacs

This writes an .itp topology and separate parameter file (in the case of 
additional parameters being needed).  Then you simply #include those files, a 
topic that comes up seemingly every day on this list.

-Justin

> Thanks,
> Soumya
>
>
> On 3/17/16 8:04 PM, Soumya Lipsa Rath wrote:
>>> Dear Justin,
>>>
>>> Thanks for your reply. I meant, that the PRODRG server gave error in
>> giving
>>> the topology file since my inhibitor contains a metal which the server
>>> doesn't process. If PRODRG is meant for GROMOS, should I use CGENFF for
>>> CHARMM? In that case, how do we include the topology of the inhibitor
>>> during the protein-ligand simulation?
>>>
>>
>> Yes, you should use CGenFF when using the CHARMM force field.  They're
>> compatible by design.
>>
>> But I can't guarantee that you'll even be able to create a topology;
>> CGenFF is
>> for organic molecules.  Any metal parameters would have to come from CHARMM
>> itself, but you still haven't told me what that metal is so I don't know if
>> CHARMM will cover it...
>>
>> -Justin
>>
>>> Thanks,
>>> Soumya
>>>
>>>>
>>>>
>>>> On 3/16/16 10:18 PM, Soumya Lipsa Rath wrote:
>>>>> Dear Gromacs Users,
>>>>>
>>>>> I have to run a protein-ligand system. I am using CHARMM36 ff for the
>>>>> simulation. For generating the parameters for the ligand molecule I
>> used
>>>>> the forcefield development toolkit of vmd, which gives CHARMM
>> compatible
>>>>> parameters.
>>>>>
>>>>> But, I am unable to understand how should I include the parameters I
>> had
>>>>> obtained. I went through the tutorial files which shows an example of
>>>>> PRODRG server for generating the itp file, but my ligand contains metal
>>>>> atoms. I would appreciate if somebody could suggest me how to solve
>> this.
>>>>>
>>>>
>>>> What are the ligands?  What metal?
>>>>
>>>> Don't use PRODRG; it's only intended for GROMOS force fields (and even
>>>> then, the
>>>> topologies need a lot of work).
>>>>
>>>> -Justin
>>>>
>>>> --
>>>> ==================================================
>>>>
>>>> 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
>>>>
>>>> ==================================================
>>>>
>>>>
>>>>
>>>>
>>
>> --
>> ==================================================
>>
>> 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
>>
>> ==================================================
>>
>>
>>

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

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

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