[gmx-users] Using pdb2gmx with martini (coarse-grained) model to assign termini charges

[Tsjerk Wassenaar]

Hi Sourav,

For Martini there's the conversion script martinize, which has an option
-nt to suppress putting charges on termini.

This is not really a Gromacs question, and it's better to post Martini
related questions on the forum at http://cgmartini.nl

Cheers,

Tsjerk
On May 24, 2016 23:35, "Justin Lemkul" <jalemkul at vt.edu> wrote:

>
>
> On 5/24/16 5:33 PM, Sourav Ray wrote:
>
>> Hello
>>
>> Thanks for your answer, I presume pdb2gmx needs some force-field
>> definitions to work, anyway, can I assign charges selectively to certain
>> atom  number? Let me know if it is feasible, I searched the forums but
>> couldn't find anything specific.
>>
>>
> Try some MARTINI tutorials; IIRC topology generation is not typically done
> via pdb2gmx.
>
> -Justin
>
> Regards
>> Sourav
>>
>> On Wed, May 25, 2016 at 2:48 AM, Mark Abraham <mark.j.abraham at gmail.com>
>> wrote:
>>
>> Hi,
>>>
>>> If you've already arranged your own termini, then you can choose "None"
>>> from the options pdb2gmx presents.
>>>
>>> Mark
>>>
>>> On Tue, May 24, 2016 at 11:15 PM Sourav Ray <souravray90 at gmail.com>
>>> wrote:
>>>
>>> Hello
>>>>
>>>> I am trying to put selective charges on the termini, I am getting stuck
>>>>
>>> at
>>>
>>>> the initial stage where I am supposed to mention the force-field needed.
>>>>
>>> As
>>>
>>>> martini termini differ from conventional ones, I am unable to bypass
>>>> NH3+
>>>> or COO- termini options at the start and end respectively as there is no
>>>> appropriate force-field option present there. Please let me know if
>>>>
>>> anyone
>>>
>>>> has a workaround.
>>>>
>>>> Regards
>>>> Sourav
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> --
> ==================================================
>
> Justin A. Lemkul, Ph.D.
> Ruth L. Kirschstein NRSA Postdoctoral Fellow
>
> Department of Pharmaceutical Sciences
> School of Pharmacy
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