[gmx-users] Regarding gromacs commands..

[Dilip H N]

can i create it with Avogadro molecular editor software..??
I tried creating using this software,, than if i compile it and run the
command of mdrun......
it is giving segmentation fault....
how to rectify it..??



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On Sat, Jan 7, 2017 at 12:15 AM, Justin Lemkul <jalemkul at vt.edu> wrote:

>
>
> On 1/6/17 2:24 AM, Dilip H N wrote:
>
>> no...
>> I want to create  300 molecules of ammonia...
>>
>
> Well, you asked about BF3, so you got an answer about BF3 :)
>
> how can i create  300 molecules of ammonia and then get it in .pdb file
>> format..??
>>
>>
> For a simple molecule like NH3 you can easily write the coordinates by
> hand from basic geometry.  Otherwise, find an NMR structure of a protein
> that contains Lys and copy its NZ-HZ[123] group and use that.  gmx
> insert-molecules -nmol 300 will give you a box of 300.
>
> -Justin
>
>
>>
>>  Sent with Mailtrack
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>> ral=cy16f01.dilip at nitk.edu.in&idSignature=22>
>>
>> On Fri, Jan 6, 2017 at 11:01 AM, Alex <nedomacho at gmail.com> wrote:
>>
>> Google "bf3 rcsb" > third result from the top
>>> https://www3.rcsb.org/ligand/BF3 > download cif file (view/download on
>>> the right) > open in pymol > save as pdb
>>>
>>> Alex
>>>
>>>
>>> On 1/5/2017 10:20 PM, Dilip H N wrote:
>>>
>>> I want to do a simulation of BF3 molecule..
>>>> how can i create a pdb file of BF3 molecule..??
>>>> is there any softwares for creating a .pdb files ..??
>>>>
>>>>
>>>>
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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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-- 
With Best Regards,

DILIP.H.N
Ph.D Student,
Research Scholar,
Department of Chemistry,
National Institute of Technology-Karnataka,
Surathkal, Mangaluru - 575025.