[gmx-users] Charmm 36 parameter file for gromacs

[Vy Phan]

Dear Dr Justin and Gromacs User,
As I mentioned in the previous email , I download the parameter from this
website which was build for all-atom simulation (
http://mmkluster.fos.su.se/slipids/Downloads.html ). I attached the file
below . I have a confusion with Tielema's website. I use this for run
membrane protein simulations and it work well, no errors like the topology
which was embedded in charmm36 force field for with Gromacs format.

I just want to ask why I got many error when I use the topology which was
embedded in charmm36 force field for with Gromacs format? Some suggestion
to me please.

Dear Dr. Justin
Thank you so much for your suggestion. I will try with CHARMM-GUI.

Best regards,
Tuong Vy

2015-08-12 21:19 GMT+09:00 Vy Phan <phanvy120690 at gmail.com>:

> Dear Dr Justin and Gromacs User,
> As I mentioned in the previous email , I download the parameter from this
> website which was build for all-atom simulation (
> http://mmkluster.fos.su.se/slipids/Downloads.html ). I attached the file
> below . I have a confusion with Tielema's website. I use this for run
> membrane protein simulations and it work well, no errors like the topology
> which was embedded in charmm36 force field for with Gromacs format.
>
> I just want to ask why I got many error when I use the topology which was
> embedded in charmm36 force field for with Gromacs format? Some suggestion
> to me please.
>
> Dear Dr. Justin
> Thank you so much for your suggestion. I will try with CHARMM-GUI.
>
> Best regards,
> Tuong Vy
>
> 2015-08-12 20:32 GMT+09:00 Justin Lemkul <jalemkul at vt.edu>:
>
>>
>>
>> On 8/11/15 10:15 PM, Vy Phan wrote:
>>
>>> Dear Dr. Justin and Gromacs User,
>>>
>>> Thank you so much for your helps.
>>>
>>> When I use charmm36 ff to generate the topology for lipid (DOPC). I got
>>> many warning "Warning :Long bond "
>>> And after get the topology, the total charge is very high (+888 e for
>>> DOPC
>>> bilayer have 516 molecular). When I used grompp to generate the .tpr
>>> file,
>>> I got the many error like this  :
>>> Error  3379 [file topol_Other_chain_D.itp, line 198252]
>>>   No defaut U-B types
>>> ...
>>> Error  2379 [file topol_Other_chain_D.itp, line 98252]
>>>    No default Proper Dih.type
>>> ....
>>>
>>> What can I do to modified the topology to get the correct charge and  fix
>>> the error ?
>>>
>>> I download dopc.itp from Tieleman's website. I run simulation and all
>>> things look fine.  People have experiences, please tell  me the
>>> difference
>>> of this topology and the one on the charmm36 force field.
>>>
>>>
>> The files Tieleman provides are united-atom structures that may use a
>> different naming convention.  They won't have H atoms on the aliphatic
>> groups and there is no .hdb entry for DOPC.  The ridiculous net charge you
>> got for DOPC (which is neutral!) should be an indicator that whatever
>> topology you built is utter nonsense.  There should also be no warnings
>> about missing parameters, so this is further evidence that the topology is
>> wrong and the "things look fine" assertion seems totally unfounded to me.
>>
>> If you want to simulate a simple membrane, use CHARMM-GUI to build it.
>> It will be 100% CHARMM compliant and we give you all the necessary input
>> files.
>>
>>
>> -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
>>
>> ==================================================
>> --
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