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

[Justin Lemkul]

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
>>> --
>>> Gromacs Users mailing list
>>>
>>> * Please search the archive at
>>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>>> posting!
>>>
>>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>>
>>> * For (un)subscribe requests visit
>>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>>> send a mail to gmx-users-request at gromacs.org.
>>>
>> --
>> Gromacs Users mailing list
>>
>> * Please search the archive at
>> http://www.gromacs.org/Support/Mailing_Lists/GMX-Users_List before
>> posting!
>>
>> * Can't post? Read http://www.gromacs.org/Support/Mailing_Lists
>>
>> * For (un)subscribe requests visit
>> https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
>> send a mail to gmx-users-request at gromacs.org.
>>

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

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

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