Re: [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"  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 
>> 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 
>>> 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
> Health Sciences Facility II, Room 629
> University of Maryland, Baltimore
> 20 Penn St.
> Baltimore, MD 21201
>
> jalem...@outerbanks.umaryland.edu | (410) 706-7441
> http://mackerell.umaryland.edu/~jalemkul
>
> ==
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Re: [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 
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  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
Health Sciences Facility II, Room 629
University of Maryland, Baltimore
20 Penn St.
Baltimore, MD 21201

jalem...@outerbanks.umaryland.edu | (410) 706-7441
http://mackerell.umaryland.edu/~jalemkul

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

[Sourav Ray]

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.

Regards
Sourav

On Wed, May 25, 2016 at 2:48 AM, Mark Abraham 
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  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
> >
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> > https://maillist.sys.kth.se/mailman/listinfo/gromacs.org_gmx-users or
> > send a mail to gmx-users-requ...@gromacs.org.
> >
> --
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[gmx-users] Using pdb2gmx with martini (coarse-grained) model to assign termini charges

[Sourav Ray]

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

[Mark Abraham]

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  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-requ...@gromacs.org.
>
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[gmx-users] Using pdb2gmx with martini (coarse-grained) model to assign termini charges

[Sourav Ray]

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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