[gmx-users] Doubt from topology creation

[rakesh.pant at students.iiserpune.ac.in]

Dear Justin
Just to learn how g-x2top works.

Thanks


Sent from my Windows 10 phone

From: Justin Lemkul
Sent: 22 February 2017 00:38
To: gmx-users at gromacs.org
Subject: Re: [gmx-users] Doubt from topology creation



On 2/21/17 2:06 PM, rakesh.pant at students.iiserpune.ac.in wrote:
> Dear Justin,
>
> But is it possible to do with g-x2top.
>

Sure, but why do something the hard way when there is a much easier way?

-Justin

> Thanks
>
> Sent from my Windows 10 phone
>
> From: Justin Lemkul
> Sent: 22 February 2017 00:27
> To: gmx-users at gromacs.org
> Subject: Re: [gmx-users] Doubt from topology creation
>
>
>
> On 2/21/17 1:27 PM, Rakesh Pant wrote:
>> Dear Justin
>>
>> I am sharing the link, please have a look.
>>
>> https://www.dropbox.com/s/b1czeuf9hbrjwxi/atomname2type.n2t?dl=0
>> https://www.dropbox.com/s/b8mfxktucuqge5k/file.pdb?dl=0
>> https://www.dropbox.com/s/7v58inob81ogo3m/to.top?dl=0
>>
>
> I wouldn't both using g_x2top for something as simple as imidazole.  Just take
> the existing histidine side chain and use it as the basis for an imidazole
> residue.  The atom types used in HISD/HISE are redundant with what you're using
> (same LJ) so it's straightforward to create an .rtp entry and have pdb2gmx build
> the topology.
>
> -Justin
>
>> Thanks
>>
>>
>>
>>
>> On Tue, Feb 21, 2017 at 11:30 PM, Justin Lemkul <jalemkul at vt.edu> wrote:
>>
>>>
>>>
>>> On 2/21/17 10:05 AM, Rakesh Pant wrote:
>>>
>>>> Dear all,
>>>>
>>>> I am trying to create a topology for a molecule using g_x2top and have
>>>> defined all the atoms with connectivity in *atomname.n2t* file with
>>>> different opls no. for all different types of atoms.
>>>>
>>>> But when I create topology, it does not identify all different atomtypes
>>>> and takes one common opls no. for some of the atoms.
>>>>
>>>> I have attached the pdb file and .n2t file.
>>>>
>>>>
>>> The list does not accept attachments.  If you want to share files, upload
>>> them to a file-sharing service and provide the URL.
>>>
>>> -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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