[gmx-users] Charmm 36 parameter file for gromacs

[Vy Phan]

Dear Dr. Justin
I got your means and it is very helpful for me.
Thank you so much :)

Sincerely,
Tuong Vy


2015-08-12 21:23 GMT+09:00 Justin Lemkul <jalemkul at vt.edu>:

>
>
> On 8/12/15 8:20 AM, Vy Phan wrote:
>
>> 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
>>
>
> The list does not accept attachments, not is it necessary.
>
> 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.
>>
>>
> Previous success with a different force field has no bearing on future
> success with a different model that uses a different convention (all-atom
> vs. united-atom).
>
> 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.
>>
>>
> As I said before, you have serious problems with whatever topology you
> managed to generate.  A charge of +888 on a 516-lipid DOPC (which is
> neutral) is total nonsense, so you certainly have missing or incorrect
> atoms that you've bypassed with pdb2gmx options or something else.
> Whatever that topology has in it is certainly wrong and should not be used.
>
> -Justin
>
>
> 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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>>>>
>>>
>>>
> --
> ==================================================
>
> 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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