[gmx-users] Charmm 36 parameter file for gromacs

[Justin Lemkul]

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

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